Extraction of Airways with Probabilistic State-space Models and Bayesian Smoothing

Segmenting tree structures is common in several image processing applications. In medical image analysis, reliable segmentations of airways, vessels, neurons and other tree structures can enable important clinical applications. We present a framework for tracking tree structures comprising of elongated branches using probabilistic state-space models and Bayesian smoothing. Unlike most existing methods that proceed with sequential tracking of branches, we present an exploratory method, that is less sensitive to local anomalies in the data due to acquisition noise and/or interfering structures. The evolution of individual branches is modelled using a process model and the observed data is incorporated into the update step of the Bayesian smoother using a measurement model that is based on a multi-scale blob detector. Bayesian smoothing is performed using the RTS (Rauch-Tung-Striebel) smoother, which provides Gaussian density estimates of branch states at each tracking step. We select likely branch seed points automatically based on the response of the blob detection and track from all such seed points using the RTS smoother. We use covariance of the marginal posterior density estimated for each branch to discriminate false positive and true positive branches. The method is evaluated on 3D chest CT scans to track airways. We show that the presented method results in additional branches compared to a baseline method based on region growing on probability images.Comment: 10 pages. Pre-print of the paper accepted at Workshop on Graphs in Biomedical Image Analysis. MICCAI 2017. Quebec Cit

Compositional Design and Verification of a Multi-Agent System for One-to-Many Negotiation

A compositional verification method for multi-agent systems is presented and applied to a multi-agent system for one-to-many negotiation in the domain of load balancing of electricity use. Advantages of the method are that the complexity of the verification process is managed by compositionality, and that parts of the proofs can be reused in relation to reuse of components

Modeling software design diversity

Design diversity has been used for many years now as a means of achieving a degree of fault tolerance in software-based systems. Whilst there is clear evidence that the approach can be expected to deliver some increase in reliability compared with a single version, there is not agreement about the extent of this. More importantly, it remains difficult to evaluate exactly how reliable a particular diverse fault-tolerant system is. This difficulty arises because assumptions of independence of failures between different versions have been shown not to be tenable: assessment of the actual level of dependence present is therefore needed, and this is hard. In this tutorial we survey the modelling issues here, with an emphasis upon the impact these have upon the problem of assessing the reliability of fault tolerant systems. The intended audience is one of designers, assessors and project managers with only a basic knowledge of probabilities, as well as reliability experts without detailed knowledge of software, who seek an introduction to the probabilistic issues in decisions about design diversity

PHI-base update: additions to the pathogen–host interaction database

The pathogen–host interaction database (PHI-base) is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and Oomycete pathogens, which infect human, animal, plant, insect, fish and fungal hosts. Plant endophytes are also included. PHI-base is therefore an invaluable resource for the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. The database is freely accessible to both academic and non-academic users. This publication describes recent additions to the database and both current and future applications. The number of fields that characterize PHI-base entries has almost doubled. Important additional fields deal with new experimental methods, strain information, pathogenicity islands and external references that link the database to external resources, for example, gene ontology terms and Locus IDs. Another important addition is the inclusion of anti-infectives and their target genes that makes it possible to predict the compounds, that may interact with newly identified virulence factors. In parallel, the curation process has been improved and now involves several external experts. On the technical side, several new search tools have been provided and the database is also now distributed in XML format. PHI-base is available at: http://www.phi-base.org/

Segmentation of Loops from Coronal EUV Images

We present a procedure which extracts bright loop features from solar EUV images. In terms of image intensities, these features are elongated ridge-like intensity maxima. To discriminate the maxima, we need information about the spatial derivatives of the image intensity. Commonly, the derivative estimates are strongly affected by image noise. We therefore use a regularized estimation of the derivative which is then used to interpolate a discrete vector field of ridge points ``ridgels'' which are positioned on the ridge center and have the intrinsic orientation of the local ridge direction. A scheme is proposed to connect ridgels to smooth, spline-represented curves which fit the observed loops. Finally, a half-automated user interface allows one to merge or split, eliminate or select loop fits obtained form the above procedure. In this paper we apply our tool to one of the first EUV images observed by the SECCHI instrument onboard the recently launched STEREO spacecraft. We compare the extracted loops with projected field lines computed from almost-simultaneously-taken magnetograms measured by the SOHO/MDI Doppler imager. The field lines were calculated using a linear force-free field model. This comparison allows one to verify faint and spurious loop connections produced by our segmentation tool and it also helps to prove the quality of the magnetic-field model where well-identified loop structures comply with field-line projections. We also discuss further potential applications of our tool such as loop oscillations and stereoscopy.Comment: 13 pages, 9 figures, Solar Physics, online firs

Programmed cell death in host-symbiont associations, viewed through the Gene Ontology

Manipulation of programmed cell death (PCD) is central to many host microbe interactions. Both plant and animal cells use PCD as a powerful weapon against biotrophic pathogens, including viruses, which draw their nutrition from living tissue. Thus, diverse biotrophic pathogens have evolved many mechanisms to suppress programmed cell death, and mutualistic and commensal microbes may employ similar mechanisms. Necrotrophic pathogens derive their nutrition from dead tissue, and many produce toxins specifically to trigger programmed cell death in their hosts. Hemibiotrophic pathogens manipulate PCD in a most exquisite way, suppressing PCD during the biotrophic phase and stimulating it during the necrotrophic phase. This mini-review will summarize the mechanisms that have evolved in diverse microbes and hosts for controlling PCD and the Gene Ontology terms developed by the Plant-Associated Microbe Gene Ontology (PAMGO) Consortium for describing those mechanisms