Phylodynamic analysis of an emergent Mycobacterium bovis outbreak in an area with no previously known wildlife infections

1. Understanding how an emergent pathogen successfully establishes itself and persists in a previously unaffected population is a crucial problem in disease ecology, with important implications for disease management. In multi-host pathogen systems this problem is particularly difficult, as the importance of each host species to transmission is often poorly characterised, and the disease epidemiology is complex. Opportunities to observe and analyse such emergent scenarios are few. 2. Here, we exploit a unique dataset combining densely-collected data on the epidemiological and evolutionary characteristics of an outbreak of Mycobacterium bovis (the causative agent of bovine tuberculosis, bTB) in a population of cattle and badgers in an area considered low-risk for bTB, with no previous record of either persistent infection in cattle, or of any infection in wildlife. We analyse the outbreak dynamics using a combination of mathematical modelling, Bayesian evolutionary analyses, and machine learning. 3. Comparison to M. bovis whole-genome sequences from Northern Ireland confirmed this to be a single introduction of the pathogen from the latter region, with evolutionary analysis supporting an introduction directly into the local cattle population six years prior to its first discovery in badgers. 4. Once introduced, the evidence supports M. bovis epidemiological dynamics passing through two phases, the first dominated by cattle-to-cattle transmission before becoming established in the local badger population. 5. Synthesis and applications. The raw data object of this analysis were used to support decisions regarding the control of a M. bovis emergent outbreak, of considerable concern because of the geographical distance from previously known high-risk areas. Our further analyses, estimating the time of introduction (and therefore the likely magnitude of any hidden outbreak) and the rates of cross-species transmission, provided valuable confirmation that the extent and focus of the imposed controls were appropriate. Not only these findings strengthen the call for genomic surveillance, but they also pave the path for future outbreaks control, providing insights for more rapid and decisive evidence-based decision-making. As the methods we used and developed are agnostic to the disease itself, they are also valuable for other slowly transmitting pathogens

Developing independent investigators for clinical research relevant for Africa

Sustainable research capacity building requires training individuals at multiple levels within a supportive institutional infrastructure to develop a critical mass of independent researchers. At many African medical institutions, a PhD is important for academic promotion and is, therefore, an important focal area for capacity building programs. We examine the training at the Infectious Diseases Institute (IDI) as a model for in-country training based on systems capacity building and attention to the academic environment. PhD training in Africa should provide a strong research foundation for individuals to perform independent, original research and to mentor others. Training the next generation of researchers within excellent indigenous academic centers of excellence with strong institutional infrastructure will empower trainees to ask regionally relevant research questions that will benefit Africans

The SAMI Galaxy Survey: Environmental analysis of the orbital structures of passive galaxies

Most dynamical models of galaxies to date assume axisymmetry, which is not representative of a significant fraction of massive galaxies. We have built triaxial orbit-superposition Schwarzschild models of galaxies observed by the SAMI Galaxy Survey, in order to reconstruct their inner orbital structure and mass distribution. The sample consists of 153 passive galaxies with total stellar masses in the range $10^{9.5}$ to $10^{12} M_{\odot}$. We present an analysis of the internal structures and intrinsic properties of these galaxies as a function of their environment. We measure their environment using three proxies: central or satellite designation, halo mass and local $5^{th}$ nearest neighbour galaxy density. We find that although these intrinsic properties correlate most strongly with stellar mass, environment does play a secondary role: at fixed stellar mass, galaxies in the densest regions are more radially anisotropic. In addition, central galaxies, and galaxies in high local densities show lower values of edge-on spin parameter proxy \lam. We also find suggestions of a possible trend of the fractions of orbits with environment for lower-mass galaxies (between $10^{9.5}$ and $10^{11} M_{\odot}$) such that, at fixed stellar mass, galaxies in higher local densities and halo mass have higher fractions of hot orbits and lower fractions of warm orbits. Our results demonstrate that after stellar mass, environment does play a role in shaping present-day passive galaxies.Comment: 21 pages. Accepted for publication in MNRA

The accretion histories of brightest cluster galaxies from their stellar population gradients

We analyse the spatially-resolved stellar populations of 9 local ($z<0.1$) Brightest Cluster Galaxies (BCGs) observed with VIMOS in IFU mode. Our sample is composed of 7 slow-rotating and 2 fast-rotating BCGs. We do not find a connection between stellar kinematics and stellar populations in this small sample. The BCGs have shallow metallicity gradients (median $\Delta$[Fe/H] $= -0.11\pm0.1$), high central metallicities (median $[$Fe/H]$_{[\alpha/Fe]=0} = 0.13\pm0.07$), and a wide range of central ages (from 5 to 15 Gyr). We propose that the reason for this is diverse evolutionary paths in BCGs. 67 per cent of the sample (6/9) show $\sim 7$ Gyr old central ages, which reflects an active accretion history, and 33 per cent of the sample (3/9) have central ages older than 11 Gyr, which suggest no star formation since $z=2$. The BCGs show similar central stellar populations and stellar population gradients to early-type galaxies of similar mass (M$_{dyn}> 10^{11.3}$M$_{\odot}$) from the ATLAS$^{3D}$ survey (median [Z/H] $= 0.04\pm0.07$, $\Delta$[Z/H] $= -0.19\pm0.1$). However, massive early-type galaxies from ATLAS$^{3D}$ have consistently old ages (median Age $=12.0\pm3.8$Gyr). We also analyse the close massive companion galaxies of two of the BCGs. These galaxies have similar stellar populations to their respective BCGs.Comment: Accepted for publication, MNRAS, March 3, 201

The SAMI Galaxy Survey: Quenching of Star Formation in Clusters I. Transition Galaxies

We use integral-field spectroscopy from the SAMI Galaxy Survey to identify galaxies that show evidence of recent quenching of star formation. The galaxies exhibit strong Balmer absorption in the absence of ongoing star formation in more than 10% of their spectra within the SAMI field of view. These Hd-strong (HDS) galaxies (HDSGs) are rare, making up only similar to 2% (25/1220) of galaxies with stellar mass log(M-*/M-circle dot) &gt; 10. The HDSGs make up a significant fraction of nonpassive cluster galaxies (15%; 17/115) and a smaller fraction (2.0%; 8/387) of the nonpassive population in low-density environments. The majority (9/17) of cluster HDSGs show evidence of star formation at their centers, with the HDS regions found in the outer parts of the galaxy. Conversely, the HDS signal is more evenly spread across the galaxy for the majority (6/8) of HDSGs in low-density environments and is often associated with emission lines that are not due to star formation. We investigate the location of the HDSGs in the clusters, finding that they are exclusively within 0.6R(200) of the cluster center and have a significantly higher velocity dispersion relative to the cluster population. Comparing their distribution in projected phase space to those derived from cosmological simulations indicates that the cluster HDSGs are consistent with an infalling population that has entered the central 0.5r(200,3D) cluster region within the last similar to 1 Gyr. In the eight of nine cluster HDSGs with central star formation, the extent of star formation is consistent with that expected of outside-in quenching by ram pressure stripping. Our results indicate that the cluster HDSGs are currently being quenched by ram pressure stripping on their first passage through the cluster

Galaxy And Mass Assembly (GAMA): stellar mass growth of spiral galaxies in the cosmic web

We look for correlated changes in stellar mass and star formation rate (SFR) along filaments in the cosmic web by examining the stellar masses and UV-derived SFRs of 1799 ungrouped and unpaired spiral galaxies that reside in filaments. We devise multiple distance metrics to characterize the complex geometry of filaments, and find that galaxies closer to the cylindrical centre of a filament have higher stellar masses than their counterparts near the periphery of filaments, on the edges of voids. In addition, these peripheral spiral galaxies have higher SFRs at a given mass. Complementing our sample of filament spiral galaxies with spiral galaxies in tendrils and voids, we find that the average SFR of these objects in different large-scale environments are similar to each other with the primary discriminant in SFR being stellar mass, in line with previous works. However, the distributions of SFRs are found to vary with large-scale environment. Our results thus suggest a model in which in addition to stellar mass as the primary discriminant, the large-scale environment is imprinted in the SFR as a second-order effect. Furthermore, our detailed results for filament galaxies suggest a model in which gas accretion from voids on to filaments is primarily in an orthogonal direction. Overall, we find our results to be in line with theoretical expectations of the thermodynamic properties of the intergalactic medium in different large-scale environments

Adenocarcinoma of the caecum metastatic to the bladder: an unusual cause of haematuria

BACKGROUND: Primary malignancies of colorectal origin can metastasise to the bladder. Reports are however extremely rare, particularly from the caecum. CASE REPORT: The report describes the case of a 45-year old male with Duke's B caecal carcinoma treated with a laparoscopically-assisted right hemicolectomy and adjuvant 5-Fluorouracil chemotherapy. Subsequently, a metastatic lesion to the bladder was demonstrated and successfully excised by partial cystectomy. CONCLUSION: In order that optimal therapeutic options can be determined, it is important for clinicians to distinguish between primary disease of the bladder and other causes of haematuria. Various immunohistochemical techniques attempt to differentiate primary adenocarcinoma of the bladder from secondary colorectal adenocarcinoma. Suspicion of metastatic disease must be raised when histologically unusual bladder tumours are identified

Deep Investigation of Neutral Gas Origins (DINGO): HI stacking experiments with early science data

We present early science results from Deep Investigation of Neutral Gas Origins (DINGO), an HI survey using the Australian Square Kilometre Array Pathfinder (ASKAP). Using ASKAP sub-arrays available during its commissioning phase, DINGO early science data were taken over $\sim$ 60 deg$^{2}$ of the Galaxy And Mass Assembly (GAMA) 23 h region with 35.5 hr integration time. We make direct detections of six known and one new sources at $z < 0.01$. Using HI spectral stacking, we investigate the HI gas content of galaxies at $0.04 < z< 0.09$ for different galaxy colours. The results show that galaxy morphology based on optical colour is strongly linked to HI gas properties. To examine environmental impacts on the HI gas content of galaxies, three sub-samples are made based on the GAMA group catalogue. The average HI mass of group central galaxies is larger than those of satellite and isolated galaxies, but with a lower HI gas fraction. We derive a variety of HI scaling relations for physical properties of our sample, including stellar mass, stellar mass surface density, $NUV-r$ colour, specific star formation rate, and halo mass. We find that the derived HI scaling relations are comparable to other published results, with consistent trends also observed to $\sim$0.5 dex lower limits in stellar mass and stellar surface density. The cosmic HI densities derived from our data are consistent with other published values at similar redshifts. DINGO early science highlights the power of HI spectral stacking techniques with ASKAP.Comment: 27 pages, 25 figures, 10 tables, accepted for publication in MNRA