A Note on Encodings of Phylogenetic Networks of Bounded Level

Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of level-k networks, k a non-negative integer, it is natural to wonder whether our arguments could be extended to members of that hierarchy for higher values for k. By giving examples, we show that this is not the case

Should We Learn Probabilistic Models for Model Checking? A New Approach and An Empirical Study

Many automated system analysis techniques (e.g., model checking, model-based testing) rely on first obtaining a model of the system under analysis. System modeling is often done manually, which is often considered as a hindrance to adopt model-based system analysis and development techniques. To overcome this problem, researchers have proposed to automatically "learn" models based on sample system executions and shown that the learned models can be useful sometimes. There are however many questions to be answered. For instance, how much shall we generalize from the observed samples and how fast would learning converge? Or, would the analysis result based on the learned model be more accurate than the estimation we could have obtained by sampling many system executions within the same amount of time? In this work, we investigate existing algorithms for learning probabilistic models for model checking, propose an evolution-based approach for better controlling the degree of generalization and conduct an empirical study in order to answer the questions. One of our findings is that the effectiveness of learning may sometimes be limited.Comment: 15 pages, plus 2 reference pages, accepted by FASE 2017 in ETAP

Modelling Hurricane Exposure and Wind Speed on a Mesoclimate Scale: A Case Study from Cusuco NP, Honduras

High energy weather events are often expected to play a substantial role in biotic community dynamics and large scale diversity patterns but their contribution is hard to prove. Currently, observations are limited to the documentation of accidental records after the passing of such events. A more comprehensive approach is synthesising weather events in a location over a long time period, ideally at a high spatial resolution and on a large geographic scale. We provide a detailed overview on how to generate hurricane exposure data at a meso-climate level for a specific region. As a case study we modelled landscape hurricane exposure in Cusuco National Park (CNP), Honduras with a resolution of 50 m×50 m patches. We calculated actual hurricane exposure vulnerability site scores (EVVS) through the combination of a wind pressure model, an exposure model that can incorporate simple wind dynamics within a 3-dimensional landscape and the integration of historical hurricanes data. The EVSS was calculated as a weighted function of sites exposure, hurricane frequency and maximum wind velocity. Eleven hurricanes were found to have affected CNP between 1995 and 2010. The highest EVSS's were predicted to be on South and South-East facing sites of the park. Ground validation demonstrated that the South-solution (i.e. the South wind inflow direction) explained most of the observed tree damage (90% of the observed tree damage in the field). Incorporating historical data to the model to calculate actual hurricane exposure values, instead of potential exposure values, increased the model fit by 50%

Human resources issues and Australian Disaster Medical Assistance Teams: results of a national survey of team members

Background: Calls for disaster medical assistance teams (DMATs) are likely to continue in response to international disasters. As part of a national survey, this study was designed to evaluate Australian DMAT experience in relation to the human resources issues associated with deployment.\ud \ud Methods: Data was collected via an anonymous mailed survey distributed via State and Territory representatives on the Australian Health Protection Committee, who identified team members associated with Australian DMAT deployments from the 2004 South East Asian Tsunami disaster.\ud \ud Results: The response rate for this survey was 50% (59/118). Most personnel had deployed to the Asian Tsunami affected areas with DMAT members having significant clinical and international experience. While all except one respondent stated they received a full orientation prior to deployment, only 34% of respondents (20/59) felt their role was clearly defined pre deployment. Approximately 56% (33/59) felt their actual role matched their intended role and that their clinical background was well suited to their tasks. Most respondents were prepared to be available for deployment for 1 month (34%, 20/59). The most common period of notice needed to deploy was 6–12 hours for 29% (17/59) followed by 12–24 hours for 24% (14/59). The preferred period of overseas deployment was 14–21 days (46%, 27/59) followed by 1 month (25%, 15/59) and the optimum shift period was felt to be 12 hours by 66% (39/59). The majority felt that there was both adequate pay (71%, 42/59) and adequate indemnity (66%, 39/59). Almost half (49%, 29/59) stated it was better to work with people from the same hospital and, while most felt their deployment could be easily covered by staff from their workplace (56%, 33/59) and caused an inconvenience to their colleagues (51%, 30/59), it was less likely to interrupt service delivery in their workplace (10%, 6/59) or cause an inconvenience to patients (9%, 5/59). Deployment was felt to benefit the affected community by nearly all (95%, 56/59) while less (42%, 25/59) felt that there was a benefit for their own local community. Nearly all felt their role was recognised on return (93%, 55/59) and an identical number (93%, 55/59) enjoyed the experience. All stated they would volunteer again, with 88% strongly agreeing with this statement.\ud \ud Conclusions: This study of Australian DMAT members provides significant insights into a number of human resources issues and should help guide future deployments. The preferred 'on call' arrangements, notice to deploy, period of overseas deployment and shift length are all identified. This extended period of operations needs to be supported by planning and provision of rest cycles, food, temporary accommodation and rest areas for staff. The study also suggests that more emphasis should be placed on team selection and clarification of roles. While the majority felt that there was both adequate pay and adequate indemnity, further work clarifying this, based on national conditions of service should be, and are, being explored currently by the state based teams in Australia. Importantly, the deployment was viewed positively by team members who all stated they would volunteer again, which allows the development of an experienced cohort of team members

Individual Predisposition, Household Clustering and Risk Factors for Human Infection with Ascaris lumbricoides: New Epidemiological Insights

Numerous analyses have found that people infected with roundworm (Ascaris lumbricoides) are predisposed to harbor either many or few worms. Members of the same household also tend to harbor similar numbers of worms. These phenomena are called individual predisposition and household clustering respectively. In this article, we use Bayesian methods to fit a statistical model to worm count data collected from a cohort of participants at baseline and after two rounds of re-infection following curative treatment. We show that individual predisposition is extremely weak once the clustering effect of the household has been accounted for. This suggests that predisposition is of limited importance to the epidemiology of roundworm infection. Further, we show that over half of the variability in average worm counts among households is explained by household risk factors. This implies that exposures to infectious roundworm eggs shared by household members are important determinants of household clustering. We argue that these results support the hypothesis proposed in the literature that the household is a key focus of roundworm transmission

Multi-parallel qPCR provides increased sensitivity and diagnostic breadth for gastrointestinal parasites of humans: field-based inferences on the impact of mass deworming

BACKGROUND: Although chronic morbidity in humans from soil transmitted helminth (STH) infections can be reduced by anthelmintic treatment, inconsistent diagnostic tools make it difficult to reliably measure the impact of deworming programs and often miss light helminth infections. METHODS: Cryopreserved stool samples from 796 people (aged 2-81 years) in four villages in Bungoma County, western Kenya, were assessed using multi-parallel qPCR for 8 parasites and compared to point-of-contact assessments of the same stools by the 2-stool 2-slide Kato-Katz (KK) method. All subjects were treated with albendazole and all Ascaris lumbricoides expelled post-treatment were collected. Three months later, samples from 633 of these people were re-assessed by both qPCR and KK, re-treated with albendazole and the expelled worms collected. RESULTS: Baseline prevalence by qPCR (n = 796) was 17 % for A. lumbricoides, 18 % for Necator americanus, 41 % for Giardia lamblia and 15% for Entamoeba histolytica. The prevalence was <1% for Trichuris trichiura, Ancylostoma duodenale, Strongyloides stercoralis and Cryptosporidium parvum. The sensitivity of qPCR was 98% for A. lumbricoides and N. americanus, whereas KK sensitivity was 70% and 32%, respectively. Furthermore, qPCR detected infections with T. trichiura and S. stercoralis that were missed by KK, and infections with G. lamblia and E. histolytica that cannot be detected by KK. Infection intensities measured by qPCR and by KK were correlated for A. lumbricoides (r = 0.83, p < 0.0001) and N. americanus (r = 0.55, p < 0.0001). The number of A. lumbricoides worms expelled was correlated (p < 0.0001) with both the KK (r = 0.63) and qPCR intensity measurements (r = 0.60). CONCLUSIONS: KK may be an inadequate tool for stool-based surveillance in areas where hookworm or Strongyloides are common or where intensity of helminth infection is low after repeated rounds of chemotherapy. Because deworming programs need to distinguish between populations where parasitic infection is controlled and those where further treatment is required, multi-parallel qPCR (or similar high throughput molecular diagnostics) may provide new and important diagnostic information

No cold dust within the supernova remnant Cassiopeia A

A large amount (about three solar masses) of cold (18 K) dust in the prototypical type II supernova remnant Cassiopeia A was recently reported. It was concluded that dust production in type II supernovae can explain how the large quantities (10^8 solar masses) of dust observed in the most distant quasars could have been produced within only 700 million years after the Big Bang. Foreground clouds of interstellar material, however, complicate the interpretation of the earlier submillimetre observations of Cas A. Here we report far-infrared and molecular line observations that demonstrate that most of the detected submillimetre emission originates from interstellar dust in a molecular cloud complex located in the line of sight between the Earth and Cas A, and is therefore not associated with the remnant. The argument that type II supernovae produce copious amounts of dust is not supported by the case of Cas A, which previously appeared to provide the best evidence for this possibility.Comment: 13 pages, 3 figure

Enhancer of zeste homolog 2 (EZH2) expression is an independent prognostic factor in renal cell carcinoma

Background: The enhancer of zeste homolog 2 (EZH2) gene exerts oncogene-like activities and its (over)expression has been linked to several human malignancies. Here, we studied a possible association between EZH2 expression and prognosis in patients with renal cell carcinoma (RCC). Methods: EZH2 protein expression in RCC specimens was analyzed by immunohistochemistry using a tissue microarray (TMA) containing RCC tumor tissue and corresponding normal tissue samples of 520 patients. For immunohistochemical assessment of EZH2 expression, nuclear staining quantity was evaluated using a semiquantitative score. The effect of EZH2 expression on cancer specific survival (CSS) was assessed by univariate and multivariate Cox regression analyses. Results: During follow-up, 147 patients (28%) had died of their disease, median follow-up of patients still alive was 6.0 years (range 0 - 16.1 years). EZH2 nuclear staining was present in tumor cores of 411 (79%) patients. A multivariate Cox regression analysis revealed that high nuclear EZH2 expression was an independent predictor of poor CSS (>25-50% vs. 0%: HR 2.72, p = 0.025) in patients suffering from non-metastatic RCC. Apart from high nuclear EZH2 expression, tumor stage and Fuhrman's grading emerged as significant prognostic markers. In metastatic disease, nuclear EZH2 expression and histopathological subtype were independent predictive parameters of poor CSS (EZH2: 1-5%: HR 2.63, p = 0.043, >5-25%: HR 3.35, p = 0.013, >25%-50%: HR 4.92, p = 0.003, all compared to 0%: HR 0.36, p = 0.025, respectively). Conclusions: This study defines EZH2 as a powerful independent unfavourable prognostic marker of CSS in patients with metastatic and non-metastatic RCC

The “ebb and flow” of student learning on placement

There is a rise in interest in work based learning as part of student choice at subject level in the UK (DOE 2017) but there remains an absence of specific guidance on how to best support higher education students learning on placement. An alternative HE experience in England, the degree apprenticeship, underlies the continued focus by policy in securing placement experiences for students without stipulating the type of support that is required at the ‘coal face’ of work based learning. Policy documents (UUK 2016), that urge universities to enter into partnership agreements with both employers and FE colleges to plug skills shortages, are noticeably lacking in their appreciation of the unique qualities of work based learning and how best to support students in this setting (Morley 2017a). Unfortunately, this is not unusual as placements have predominantly been an enriching ‘add on’ to the real business of academic learning in more traditional university programmes. Support initiatives, such as that described in chapter 9, are a rare appreciation of the importance of this role. Undergraduate nursing programmes currently support a 50:50 split between practice learning in clinical placements and the theory delivered at universities. Vocational degrees, such as this, provide an interesting case study as to how students can be supported in the practice environment by an appreciation of how students really learn on placement and how hidden resources can be utilised more explicitly for practice learning. During 2013 – 2015 a professional doctorate research study (Morley 2015) conducted a grounded theory study of 21 first year student nurses on their first placement to discover how they learnt ‘at work’ and the strategies they enlisted to be successful work based learners

The Vega debris disc: A view from Herschel

We present five band imaging of the Vega debris disc obtained using the Herschel Space Observatory. These data span a wavelength range of 70–500 μm with full-width half-maximum angular resolutions of 5.6–36.9”. The disc is well resolved in all bands, with the ring structure visible at 70 and 160 μm. Radial profiles of the disc surface brightness are produced, and a disc radius of 11” (~85 AU) is determined. The disc is seen to have a smooth structure thoughout the entire wavelength range, suggesting that the disc is in a steady state, rather than being an ephemeral structure caused by the recent collision of two large planetesimals