HDG-NEFEM with Degree Adaptivity for Stokes Flows

This paper presents the first degree adaptive procedure able to directly use the geometry given by a CAD model. The technique uses a hybridisable discontinuous Galerkin discretisation combined with a NURBS-enhanced rationale, completely removing the uncertainty induced by a polynomial approximation of curved boundaries that is common within an isoparametric approach. The technique is compared against two strategies to perform degree adaptivity currently in use. This paper demonstrates, for the first time, that the most extended technique for degree adaptivity can easily lead to a non-reliable error estimator if no communication with CAD software is introduced whereas if the communication with the CAD is done, it results in a substantial computing time. The proposed technique encapsulates the CAD model in the simulation and is able to produce reliable error estimators irrespectively of the initial mesh used to start the adaptive process. Several numerical examples confirm the findings and demonstrate the superiority of the proposed technique. The paper also proposes a novel idea to test the implementation of high-order solvers where different degrees of approximation are used in different elements

A unified approach for a posteriori high-order curved mesh generation using solid mechanics

The paper presents a unified approach for the a posteriori generation of arbitrary high-order curvilinear meshes via a solid mechanics analogy. The approach encompasses a variety of methodologies, ranging from the popular incremental linear elastic approach to very sophisticated non-linear elasticity. In addition, an intermediate consistent incrementally linearised approach is also presented and applied for the first time in this context. Utilising a consistent derivation from energy principles, a theoretical comparison of the various approaches is presented which enables a detailed discussion regarding the material characterisation (calibration) employed for the different solid mechanics formulations. Five independent quality measures are proposed and their relations with existing quality indicators, used in the context of a posteriori mesh generation, are discussed. Finally, a comprehensive range of numerical examples, both in two and three dimensions, including challenging geometries of interest to the solids, fluids and electromagnetics communities, are shown in order to illustrate and thoroughly compare the performance of the different methodologies. This comparison considers the influence of material parameters and number of load increments on the quality of the generated high-order mesh, overall computational cost and, crucially, the approximation properties of the resulting mesh when considering an isoparametric finite element formulation

Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists. © 2011 Hatfull et al

An explicit hybridizable discontinuous Galerkin method for the 3D time-domain Maxwell equations

International audienceWe present an explicit hybridizable discontinuous Galerkin (HDG) method for numerically solving the system of three-dimensional (3D) time-domain Maxwell equations. The method is fully explicit similarly to classical so-called DGTD (Dis-continuous Galerkin Time-Domain) methods, is also high-order accurate in both space and time and can be seen as a generalization of the classical DGTD scheme based on upwind fluxes. We provide numerical results aiming at assessing its numerical convergence properties by considering a model problem and we present preliminary results of the superconvergence property on the H curl norm

Geographic variation in breeding system and environment predicts melanin-based plumage ornamentation of male and female Kentish plovers

Sexual selection determines the elaboration of morphological and behavioural traits and thus drives the evolution of phenotypes. Sexual selection on males and females can differ between populations, especially when populations exhibit different breeding systems. A substantial body of literature describes how breeding systems shape ornamentation across species, with a strong emphasis on male ornamentation and female preference. However, whether breeding system predicts ornamentation within species and whether similar mechanisms as in males also shape the phenotype of females remains unclear. Here, we investigate how different breeding systems are associated with male and female ornamentation in five geographically distinct populations of Kentish plovers Charadrius alexandrinus. We predicted that polygamous populations would exhibit more elaborate ornaments and stronger sexual dimorphism than monogamous populations. By estimating the size and intensity of male (n = 162) and female (n = 174) melanin-based plumage ornaments, i.e. breast bands and ear coverts, we show that plumage ornamentation is predicted by breeding system in both sexes. A difference in especially male ornamentation between polygamous (darker and smaller ornaments) and monogamous (lighter and larger) populations causes the greatest sexual dimorphism to be associated with polygamy. The non-social environment, however, may also influence the degree of ornamentation, for instance through availability of food. We found that, in addition to breeding system, a key environmental parameter, rainfall, predicted a seasonal change of ornamentation in a sex-specific manner. Our results emphasise that to understand the phenotype of animals, it is important to consider both natural and sexual selection acting on both males and females

Using Scenarios to Validate Requirements through the use of Eye-Tracking in Prototyping

Research has shown that eliciting and capturing the correct behavior of systems reduces the number of defects that a system contains. A requirements engineer will model the functions of the system to gain a comprehensive understanding of the system in question. Engineers must verify the model for correctness by either having another engineer review it or build a prototype and validate with a stakeholder. However, research has shown that this form of verification can be ineffective because looking at an existing model can be suggestive and stump the development of new ideas. This paper provides an automated technique that can be used as an unbiased review of use case scenarios. Using the prototype and a scenario, a stakeholder can be guided through the use case scenario demonstrating where they expect to find the next step while their eye movements are tracked. Analysis of the eye tracking data can be used to identify missing requirements such as interaction steps that should have alternative sequences or determining problems with the flow of actions

Implementation of population screening for colorectal cancer by repeated fecal occult blood test in the Netherlands

<p>Abstract</p> <p>Background</p> <p>Colorectal cancer (CRC) is the third most prevalent type of cancer in the world. Its prognosis is closely related to the disease stage at the time of diagnosis. Early detection of symptomless CRC or precursor lesions through population screening could reduce CRC mortality. However, screening programs are only effective if enough people are willing to participate. This study aims to asses the uptake of a second round of fecal occult blood test (FOBt) based screening and to explore factors that could potentially increase this uptake.</p> <p>Methods and design</p> <p>Two years after the first screening round, 10.000 average risk persons, aged 50 to 75, will again receive an invitation to participate in immunohistochemical FOBt (iFOBt) based screening. Eligible persons will be recruited through a city population database. Invitees will be randomized to receive either an iFOBt with a faeces collection paper or an iFOBt without a collection paper. The iFOBts will be analyzed in a specialized laboratory at the Academic Medical Centre. Positive iFOBts will be followed by a consultation at our outpatient clinic and, in the absence of contra-indications and after informed consent, by a colonoscopy. The primary outcome measure is the participation rate. Secondary outcome measures are the effect of the addition of a collection paper on the participation rate, reasons for participation and non-participation, measures of informed choice and psychological consequences of screening and measures of psychological and physical burden associated with the iFOBt and the colonoscopy. Another secondary outcome measure is the diagnostic yield of the program.</p> <p>Discussion</p> <p>In order to implement population screening for colorectal cancer in the Netherlands, information is needed on the uptake of repeated rounds of FOBt-based screening and on factors that could potentially increase this uptake in the future since effectiveness of such a program depends on the willingness of persons to participate. This study will provide information on the actual uptake and perception of a second round of iFOBt-based screening. The results of this study will contribute to the future implementation of a national colorectal screening program in the Netherlands.</p> <p>Trial registration</p> <p>Dutch Trial register: NTR1327</p

Paternity of Subordinates Raises Cooperative Effort in Cichlids

Background In cooperative breeders, subordinates generally help a dominant breeding pair to raise offspring. Parentage studies have shown that in several species subordinates can participate in reproduction. This suggests an important role of direct fitness benefits for cooperation, particularly where groups contain unrelated subordinates. In this situation parentage should influence levels of cooperation. Here we combine parentage analyses and detailed behavioural observations in the field to study whether in the highly social cichlid Neolamprologus pulcher subordinates participate in reproduction and if so, whether and how this affects their cooperative care, controlling for the effect of kinship. Methodology/Principal Findings We show that: (i) male subordinates gained paternity in 27.8% of all clutches and (ii) if they participated in reproduction, they sired on average 11.8% of young. Subordinate males sharing in reproduction showed more defence against experimentally presented egg predators compared to subordinates not participating in reproduction, and they tended to stay closer to the breeding shelter. No effects of relatedness between subordinates and dominants (to mid-parent, dominant female or dominant male) were detected on parentage and on helping behaviour. Conclusions/Significance This is the first evidence in a cooperatively breeding fish species that the helping effort of male subordinates may depend on obtained paternity, which stresses the need to consider direct fitness benefits in evolutionary studies of helping behaviour