Hepatocellular Carcinoma Arising in Non-Cirrhotic Haemochromatosis

Hepatocellular carcinoma arising in a patient with genetic haemachromatosis, without cirrhosis, has only been described once previously. We present a patient with a 15 year history of genetic haemachromatosis who underwent resection of a hepatocellular carcinoma in a liver with normal architecture

A hierarchical Bayesian approach for handling missing classification data

Ecologists use classifications of individuals in categories to understand composition of populations and communities. These categories might be defined by demo- graphics, functional traits, or species. Assignment of categories is often imperfect, but frequently treated as observations without error. When individuals are observed but not classified, these “partial” observations must be modified to include the missing data mechanism to avoid spurious inference. We developed two hierarchical Bayesian models to overcome the assumption of perfect assignment to mutually exclusive categories in the multinomial distribu- tion of categorical counts, when classifications are missing. These models incorporate auxiliary information to adjust the posterior distributions of the proportions of membership in categories. In one model, we use an empirical Bayes approach, where a subset of data from one year serves as a prior for the missing data the next. In the other approach, we use a small random sample of data within a year to inform the distribution of the missing data. We performed a simulation to show the bias that occurs when partial observations were ignored and demonstrated the altered inference for the estimation of demographic ratios. We applied our models to demographic classifications of elk (Cervus elaphus nelsoni) to demonstrate improved inference for the proportions of sex and stage classes. We developed multiple modeling approaches using a generalizable nested multi- nomial structure to account for partially observed data that were missing not at random for classification counts. Accounting for classification uncertainty is important to accurately understand the composition of populations and communities in ecological studies

Detection, Localization and Characterization of Gravitational Wave Bursts in a Pulsar Timing Array

Efforts to detect gravitational waves by timing an array of pulsars have focused traditionally on stationary gravitational waves: e.g., stochastic or periodic signals. Gravitational wave bursts --- signals whose duration is much shorter than the observation period --- will also arise in the pulsar timing array waveband. Sources that give rise to detectable bursts include the formation or coalescence of supermassive black holes (SMBHs), the periapsis passage of compact objects in highly elliptic or unbound orbits about a SMBH, or cusps on cosmic strings. Here we describe how pulsar timing array data may be analyzed to detect and characterize these bursts. Our analysis addresses, in a mutually consistent manner, a hierarchy of three questions: \emph{i}) What are the odds that a dataset includes the signal from a gravitational wave burst? \emph{ii}) Assuming the presence of a burst, what is the direction to its source? and \emph{iii}) Assuming the burst propagation direction, what is the burst waveform's time dependence in each of its polarization states? Applying our analysis to synthetic data sets we find that we can \emph{detect} gravitational waves even when the radiation is too weak to either localize the source of infer the waveform, and \emph{detect} and \emph{localize} sources even when the radiation amplitude is too weak to permit the waveform to be determined. While the context of our discussion is gravitational wave detection via pulsar timing arrays, the analysis itself is directly applicable to gravitational wave detection using either ground or space-based detector data.Comment: 43 pages, 13 figures, submitted to ApJ

Shoot, shovel and shut up: cryptic poaching slows restoration of a large carnivore in Europe

Poaching is a widespread and well-appreciated problem for the conservation of many threatened species. Because poaching is illegal, there is strong incentive for poachers to conceal their activities, and consequently, little data on the effects of poaching on population dynamics are available. Quantifying poaching mortality should be a required knowledge when developing conservation plans for endangered species but is hampered by methodological challenges. We show that rigorous estimates of the effects of poaching relative to other sources of mortality can be obtained with a hierarchical state–space model combined with multiple sources of data. Using the Scandinavian wolf (Canis lupus) population as an illustrative example, we show that poaching accounted for approximately half of total mortality and more than two-thirds of total poaching remained undetected by conventional methods, a source of mortality we term as ‘cryptic poaching’. Our simulations suggest that without poaching during the past decade, the population would have been almost four times as large in 2009. Such a severe impact of poaching on population recovery may be widespread among large carnivores. We believe that conservation strategies for large carnivores considering only observed data may not be adequate and should be revised by including and quantifying cryptic poaching

Data and code associated with “Supporting Adaptive Management with Ecological Forecasting: Chronic Wasting Disease in the Jackson Elk Herd”

Final_Data.zip contains several spreadsheets representing data collected by both the Wyoming Game and Fish Department and the US Fish and Wildlife Service for elk management: Jackson feedground census, 1998-2016; Harvest data, 1997-2015; Hunt area census, 1998-2016; Chronic wasting disease test results, 1998-2015. Final_Code.zip contains several Program R scripts written for data analysis and model fitting as described in the full associated article.Adaptive management has emerged as the prevailing approach for combining environmental research and management to advance science and policy. Adaptive management, as originally formulated by Carl Walters in 1986, depends on the use of Bayesian models to provide a framework to accumulate knowledge. The emergence of ecological forecasting using the Bayesian framework has provided robust tools and supports a new approach to informing adaptive management, which can be particularly useful in developing policy for managing infectious disease in wildlife. We used the potential infection of elk populations with chronic wasting disease in the Jackson Valley of Wyoming and the National Elk Refuge as a model system to show how Bayesian forecasting can support adaptive management in anticipation of management challenges. The core of our approach resembles the sex- and age-structured, discrete time models used to support management decisions on elk harvest throughout western North America. Our model differs by including stages for CWD infected and unaffected animals. We used data on population counts, sex and age classification, and CWD testing, as well as results from prior research, in a Bayesian statistical framework to predict model parameters and the number of animals in each age, sex, and disease stage over time. Initial forecasts suggested CWD may reach a mean prevalence in the population of 12%, but uncertainty in this forecast is large and we cannot rule out a mean forecasted prevalence as high as 20%. Using recruitment rates observed during the last two decades, the model predicted that a CWD prevalence of 7% in females would cause the population growth rate (l) to drop below 1, resulting in population declines even when female harvest was zero. The primary value of this ecological forecasting approach is to provide a framework to assimilate data with understanding of disease processes to enable continuous improvement in understanding the ecology of CWD and its management.Data collection was funded as part of management efforts by the Wyoming Game and Fish Department and the US Fish and Wildlife Service. Data analysis and work for publication was funded by the US Fish and Wildlife Service and the National Park Service

An Anti-Glitch in a Magnetar

Magnetars are neutron stars showing dramatic X-ray and soft $\gamma$-ray outbursting behaviour that is thought to be powered by intense internal magnetic fields. Like conventional young neutron stars in the form of radio pulsars, magnetars exhibit "glitches" during which angular momentum is believed to be transferred between the solid outer crust and the superfluid component of the inner crust. Hitherto, the several hundred observed glitches in radio pulsars and magnetars have involved a sudden spin-up of the star, due presumably to the interior superfluid rotating faster than the crust. Here we report on X-ray timing observations of the magnetar 1E 2259+586 which we show exhibited a clear "anti-glitch" -- a sudden spin down. We show that this event, like some previous magnetar spin-up glitches, was accompanied by multiple X-ray radiative changes and a significant spin-down rate change. This event, if of origin internal to the star, is unpredicted in models of neutron star spin-down and is suggestive of differential rotation in the neutron star, further supporting the need for a rethinking of glitch theory for all neutron stars

Unusual glitch activity in the RRAT J1819-1458: an exhausted magnetar?

We present an analysis of regular timing observations of the high-magnetic-field Rotating Radio Transient (RRAT) J1819$-$1458 obtained using the 64-m Parkes and 76-m Lovell radio telescopes over the past five years. During this time, the RRAT has suffered two significant glitches with fractional frequency changes of $0.6\times10^{-6}$ and $0.1\times10^{-6}$. Glitches of this magnitude are a phenomenon displayed by both radio pulsars and magnetars. However, the behaviour of J1819$-$1458 following these glitches is quite different to that which follows glitches in other neutron stars, since the glitch activity resulted in a significant long-term net decrease in the slow-down rate. If such glitches occur every 30 years, the spin-down rate, and by inference the magnetic dipole moment, will drop to zero on a timescale of a few thousand years. There are also significant increases in the rate of pulse detection and in the radio pulse energy immediately following the glitches.Comment: accepted for publication in MNRAS, 7 pages, 7 figures, 1 tabl

The High Time Resolution Universe Survey II: Discovery of 5 Millisecond Pulsars

We present the discovery of 5 millisecond pulsars found in the mid-Galactic latitude portion of the High Time Resolution Universe (HTRU) Survey. The pulsars have rotational periods from ~2.3 to ~7.5 ms, and all are in binary systems with orbital periods ranging from ~0.3 to ~150 d. In four of these systems, the most likely companion is a white dwarf, with minimum masses of ~0.2 Solar Masses. The other pulsar, J1731-1847, has a very low mass companion and exhibits eclipses, and is thus a member of the "black widow" class of pulsar binaries. These eclipses have been observed in bands centred near frequencies of 700, 1400 and 3000 MHz, from which measurements have been made of the electron density in the eclipse region. These measurements have been used to examine some possible eclipse mechanisms. The eclipse and other properties of this source are used to perform a comparison with the other known eclipsing and "black widow" pulsars. These new discoveries occupy a short-period and high-dispersion measure (DM) region of parameter space, which we demonstrate is a direct consequence of the high time and frequency resolution of the HTRU survey. The large implied distances to our new discoveries makes observation of their companions unlikely with both current optical telescopes and the Fermi Gamma-ray Space Telescope. The extremely circular orbits make any advance of periastron measurements highly unlikely. No relativistic Shapiro delays are obvious in any of the systems, although the low flux densities would make their detection difficult unless the orbits were fortuitously edge-on.Comment: 11 pages, 5 figures, 4 tables, for publication in MNRA