Evaluating demographic models for goat domestication using mtDNA sequences

Routes of migration and exchange are important factors in the debate about how the Neolithic transition spread into Europe. Studying the genetic diversity of livestock can help in tracing back some of these past events. Notably, domestic goat (Capra hircus) did not have any wild progenitors (Capra aegagrus) in Europe before their arrival from the Near East. Studies of mitochondrial DNA have shown that the diversity in European domesticated goats is a subset of that in the wild, underlining the ancestral relationship between both populations. Additionally, an ancient DNA study on Neolithic goat remains has indicated that a high level of genetic diversity was already present early in the Neolithic in northwestern Mediterranean sites. We used coalescent simulations and approximate Bayesian computation, conditioned on patterns of modern and ancient mitochondrial DNA diversity in domesticated and wild goats, to test a series of simplified models of the goat domestication process. Specifically, we ask if domestic goats descend from populations that were distinct prior to domestication. Although the models we present require further analyses, preliminary results indicate that wild and domestic goats are more likely to descend from a single ancestral wild population that was managed 11,500 years before present, and that serial founding events characterise the spread of Capra hircus into Europe.

Forward-in-Time, Spatially Explicit Modeling Software to Simulate Genetic Lineages Under Selection

SELECTOR is a software package for studying the evolution of multiallelic genes under balancing or positive selection while simulating complex evolutionary scenarios that integrate demographic growth and migration in a spatially explicit population framework. Parameters can be varied both in space and time to account for geographical, environmental, and cultural heterogeneity. SELECTOR can be used within an approximate Bayesian computation estimation framework. We first describe the principles of SELECTOR and validate the algorithms by comparing its outputs for simple models with theoretical expectations. Then, we show how it can be used to investigate genetic differentiation of loci under balancing selection in interconnected demes with spatially heterogeneous gene flow. We identify situations in which balancing selection reduces genetic differentiation between population groups compared with neutrality and explain conflicting outcomes observed for human leukocyte antigen loci. These results and three previously published applications demonstrate that SELECTOR is efficient and robust for building insight into human settlement history and evolution.

Assessing mackerel scad, Decapterus macarellus, in Cape Verde: using a Bayesian approach to biomass dynamic modelling in a data-limited situation

The fisheries for mackerel scad, Decapterus macarellus, are particularly important in Cape Verde, constituting almost 40% of total catches at the peak of the fishery in 1997 and 1998 ( 3700 tonnes). Catches have been stable at a much lower level of about 2 100 tonnes in recent years. Given the importance of mackerel scad in terms of catch weight and local food security, there is an urgent need for updated assessment. Stock assessment was carried out using a Bayesian approach to biomass dynamic modelling. In order to tackle the problem of a non-informative CPUE series, the intrinsic rate of increase, r, was estimated separately, and the ratio B-0/X, initial biomass relative to carrying capacity, was assumed based on available information. The results indicated that the current level of fishing is sustainable. The probability of collapse is low, particularly in the short-term, and it is likely that biomass may increase further above B-msy, indicating a healthy stock level. It would appear that it is relatively safe to increase catches even up to 4000 tonnes. However, the marginal posterior of r was almost identical to the prior, indicating that there is relatively low information content in CPUE. This was also the case in relation to B-0/X There have been substantial increases in fishing efficiency, which have not been adequately captured by the measure used for effort (days or trips), implying that the results may be overly optimistic and should be considered preliminary. (c) 2006 Elsevier B.V. All rights reserved.

The influence of inter-domain mobility on message stream response time in wired/wireless PROFIBUS-based networks

In previous works we have proposed a hybrid wired/wireless PROFIBUS solution where the interconnection between the heterogeneous media was accomplished through bridge-like devices with wireless stations being able to move between different wireless cells. Additionally, we had also proposed a worst-case timing analysis assuming that stations were stationary. In this paper we advance these previous works by proposing a worst-case timing analysis for the system’s message streams considering the effect of inter-cell mobility.

Evaluating P-NET message's response time with fixed priority queuing at application process level

P-NET is a multi-master fieldbus standard based on a virtual token passing scheme. In P-NET each master is allowed to transmit only one message per token visit. In the worst-case, the communication response time can be derived considering that, in each token cycle, all stations use the token to transmit a message. In this paper, we define a more sophisticated P-NET model, which considers the actual token utilisation. We then analyse the possibility of implementing a local priority-based scheduling policy to improve the real-time behaviour of P-NET.

Communication response time in P-NET networks: worst-case analysis considering the actual token utilisation

Fieldbus networks aim at the interconnection of field devices such as sensors, actuators and small controllers. Therefore, they are an effective technology upon which Distributed Computer Controlled Systems (DCCS) can be built. DCCS impose strict timeliness requirements to the communication network. In essence, by timeliness requirements we mean that traffic must be sent and received within a bounded interval, otherwise a timing fault is said to occur. P-NET is a multi-master fieldbus standard based on a virtual token passing scheme. In P-NET each master is allowed to transmit only one message per token visit, which means that in the worst-case the communication response time could be derived considering that the token is fully utilised by all stations. However, such analysis can be proved to be quite pessimistic. In this paper we propose a more sophisticated P-NET timing analysis model, which considers the actual token utilisation by different masters. The major contribution of this model is to provide a less pessimistic, and thus more accurate, analysis for the evaluation of the worst-case communication response time in P-NET fieldbus networks.

Integrating inaccessibility in response time analysis of CAN networks

Controller Area Network (CAN) is a fieldbus network suitable for small-scale Distributed Computer Controlled Systems, being appropriate for transferring short real-time messages. Nevertheless, it must be understood that the continuity of service is not fully guaranteed, since it may be disturbed by temporary periods of network inaccessibility [1]. In this paper, such temporary periods of network inaccessibility are integrated in the response time analysis of CAN networks. The achieved results emphasise that, in the presence of temporary periods of network inaccessibility, a CAN network is not able to provide different integrity levels to the supported applications, since errors in low priority messages interfere with the response time of higher priority message streams.

Response time analysis of slotted WiDom in noisy wireless channels

WiDom is a wireless prioritized medium access control protocol which offers very large number of priority levels. Hence, it brings the potential to employ non-preemptive static-priority scheduling and schedulability analysis for a wireless channel assuming that the overhead of WiDom is modeled properly. Recent research has created a new version of WiDom (we call it: Slotted WiDom) which offers lower overhead compared to the previous version. In this paper we propose a new schedulability analysis for slotted WiDom and extend it to work for message streams with release jitter. Furthermore, to provide an accurate timing analysis, we must include the effect of transmission faults on message latencies. Thus, in the proposed analysis we consider the existence of different noise sources and develop the analysis for the case where messages are transmitted under noisy wireless channels. Evaluation of the proposed analysis is done by testing the slotted WiDom in two different modes on a real test-bed. The results from the experiments provide a firm validation on our findings.

Response time analysis of COTS-Based multicores considering the contention on the shared memory bus

The current industry trend is towards using Commercially available Off-The-Shelf (COTS) based multicores for developing real time embedded systems, as opposed to the usage of custom-made hardware. In typical implementation of such COTS-based multicores, multiple cores access the main memory via a shared bus. This often leads to contention on this shared channel, which results in an increase of the response time of the tasks. Analyzing this increased response time, considering the contention on the shared bus, is challenging on COTS-based systems mainly because bus arbitration protocols are often undocumented and the exact instants at which the shared bus is accessed by tasks are not explicitly controlled by the operating system scheduler; they are instead a result of cache misses. This paper makes three contributions towards analyzing tasks scheduled on COTS-based multicores. Firstly, we describe a method to model the memory access patterns of a task. Secondly, we apply this model to analyze the worst case response time for a set of tasks. Although the required parameters to obtain the request profile can be obtained by static analysis, we provide an alternative method to experimentally obtain them by using performance monitoring counters (PMCs). We also compare our work against an existing approach and show that our approach outperforms it by providing tighter upper-bound on the number of bus requests generated by a task.

Response Time Analysis of Slotted WiDOM in Noisy Wireless Channels

International Conference on Emerging Technologies and Factory Automation (ETFA 2015), Industrial Communication Technologies and Systems, Luxembourg, Luxembourg.

Response Time Analysis for Fixed-Priority Tasks with Multiple Probabilistic Parameters

Demo presented in 12th Workshop on Models and Algorithms for Planning and Scheduling Problems (MAPSP 2015). 8 to 12, Jun, 2015. La Roche-en-Ardenne, Belgium. Extended abstract.

A Generic and Compositional Framework for Multicore Response Time Analysis

23rd International Conference on Real-Time Networks and Systems (RTNS 2015). 4 to 6, Nov, 2015, Main Track. Lille, France. Best Paper Award Nominee

Evaluation of CD4+CD25+ T lymphocyte response time kinetics in patients with chronic Chagas disease after in vitro stimulation with recombinant Trypanosoma cruzi antigens

Introduction CD4+CD25+ T lymphocytes have been implicated in the regulation of host inflammatory response against Trypanosoma cruzi, and may be involved in the clinical course of the disease. Methods Peripheral blood mononuclear cells from patients with chronic Chagas disease were cultured in the presence of T. cruzi recombinant antigens and assayed for lymphocytes at distinct time points. Results It was possible to differentiate clinical forms of chronic Chagas disease at days 3 and 5 according to presence of CD4+CD25+ T cells in cell cultures. Conclusions Longer periods of cell culture proved to be potentially valuable for prospective evaluations of CD4+CD25+ T lymphocytes in patients with chronic Chagas disease.

Inequality measurement for ordered response health data

Because self-reported health status [SRHS] is an ordered response variable, inequality measurement for SRHS data requires a numerical scale for converting individual responses into a summary statistic. The choice of scale is however problematic, since small variations in the numerical scale may reverse the ordering of a given pair of distributions of SRHS data in relation to conventional inequality indices such as the variance. This paper introduces a parametric family of inequality indices, founded on an inequality ordering proposed by Allison and Foster [Allison, R.A., Foster, J., 2004. Measuring health inequalities using qualitative data. Journal of Health Economics 23, 505-524], which satisfy a suitable invariance property with respect to the choice of numerical scale. Several key members of the parametric family are also derived, and an empirical application using data from the Swiss Health Survey illustrates the proposed methodology. [Authors]