Purpose
Automated delineation of structures and organs is a key step in medical imaging. However, due to the large number and diversity of structures and the large variety of segmentation algorithms, ...a consensus is lacking as to which automated segmentation method works best for certain applications. Segmentation challenges are a good approach for unbiased evaluation and comparison of segmentation algorithms.
Methods
In this work, we describe and present the results of the Head and Neck Auto‐Segmentation Challenge 2015, a satellite event at the Medical Image Computing and Computer Assisted Interventions (MICCAI) 2015 conference. Six teams participated in a challenge to segment nine structures in the head and neck region of CT images: brainstem, mandible, chiasm, bilateral optic nerves, bilateral parotid glands, and bilateral submandibular glands.
Results
This paper presents the quantitative results of this challenge using multiple established error metrics and a well‐defined ranking system. The strengths and weaknesses of the different auto‐segmentation approaches are analyzed and discussed.
Conclusions
The Head and Neck Auto‐Segmentation Challenge 2015 was a good opportunity to assess the current state‐of‐the‐art in segmentation of organs at risk for radiotherapy treatment. Participating teams had the possibility to compare their approaches to other methods under unbiased and standardized circumstances. The results demonstrate a clear tendency toward more general purpose and fewer structure‐specific segmentation algorithms.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
This paper introduces DILIGENT, a digital library infrastructure built by integrating digital library and Grid technologies and resources. This infrastructure allows different communities to ...dynamically build specialised digital libraries capable to support the entire e-Science knowledge production and consumption life-cycle by using shared computing, storage, content, and application resources. The paper presents some of the main software services that implement the DILIGENT system. Moreover, it exemplifies the provided features by presenting how the DILIGENT infrastructure is being exploited in supporting the activity of user communities working in the Earth Science Environmental sector.PUBLICATION ABSTRACT
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Scientific applications are more and more faced with very large volumes of data and complex, resource-intensive workflows that process or analyze these data. The recent interest in web services and ...service-oriented architectures has strongly facilitated the development of individual workflow activities as well as their composition and the distributed execution of complete workflows. However, in many applications concurrent scientific workflows may be served by multiple competing providers, with each of them offering only limited resources. At the same time, these workflows need to be executed in a predictable manner, with dedicated Quality of Service guarantees. In this paper, we introduce an approach to Advance Resource Reservation for service-oriented complex scientific workflows that optimize resource consumption based on user-defined criteria (e.g., cost or time). It exploits optimization techniques using genetic algorithms for finding optimal or near-optimal allocations in a distributed system. The approach takes into account the locality of services and in particular enforces constraints imposed by control or data flow dependencies within workflows. Finally, we provide a comprehensive evaluation of the effectiveness of the proposed approach.
WS-Agreement is a well-established and widely adopted protocol that helps service providers and consumers to agree on constraints under which a service is made available. However, the original ...protocol is limited to a simple interaction pattern for establishing agreements: the requester suggests the Quality of Service (QoS) details, the responder either accepts or declines. This is no longer sufficient when several rounds of negotiations are needed before both parties agree on the QoS level to be provided, or when an already established agreement needs to be changed based on mutual consent (renegotiation). This paper presents an extension to WS-Agreement which jointly addresses these limitations.
The increasing interest in Web services has led to a recent proliferation of service-oriented platforms for supporting Scientific Workflows in a variety of e-Science domains. These platforms mainly ...address the application-specific composition and enactment of workflows. However, since scientific workflows are characterized by complex computations and large volumes of data, non-functional criteria like Quality of Service (QoS) guarantees can significantly raise the predictability of the computations, and thus constitute an important benefit to users. This paper introduces the DWARFS vision of a distributed execution engine for Scientific Workflows which features support for QoS guarantees by making use of Advance Resource Reservations. In particular, we present the DWARFS methodology to enact workflows under QoS constraints and report on the ongoing implementation activities.
Scientific Workflows have become an important tool to perform complex calculations, especially when individual operations are made available as services in Service Oriented Architectures. At the same ...time, Quality-of-Service aspects and Advance Reservation of resources by means of Service Level Agreements (SLA) are topics that get ever-increasing attention in order to make best use of available resources in a predictable manner. The support of such SLAs at the level of workflows raises two interrelated issues pertaining (i) to the temporal prediction of reservation start time and duration of individual activities, and (ii) to the actual enforcement of resource commitments at the provider side.
In this paper, we outline our vision of a distributed workflow engine with support for SLAs and Advance Reservations. We focus on reservations addressing processing capabilities, i.e., shares of CPU power. In particular, we present a module of the system that is responsible for the enforcement of such reservations at the individual service providers’ nodes, which, by means of a Fuzzy Controller adjusting task priorities, makes sure that the SLAs are met in a fair way.
The pharmacokinetics of antipsychotic drugs has become an integral part in understanding their pharmacodynamic activity and clinical effects. In addition to metabolism aspects, carrier‐mediated ...transport, particularly secretion by ABC transporters, has been discussed as potentially relevant for this group of therapeutics. In this study, the psychoactive compounds perphenazine, flupentixol, domperidone, desmethyl clozapine, haloperidol, fluphenazine, fluvoxamine, olanzapine, levome‐promazine, perazine, desmethyl perazine, clozapine, quetiapine and amisulpride were characterized in terms of P‐glycoprotein (P‐gp) affinity and transport. Experimental methods involved a radioligand displacement assay with 3Htalinolol as radioligand and transport — as well as transport inhibition — studies of the P‐gp substrate 3Htalinolol across Caco‐2 cell monolayers. In addition, the physicochemical descriptors log P and Δlog P were determined to test potential correlations between transporter affinity and lipophilicity parameters. All of the tested antipsychotics showed affinity to P‐gp albeit their IC50 values (concentration of competitor that displaced 50% of the bound radioligand) differed by a factor exceeding 1000, when compared using the transport inhibition assay. From the group of P‐gp substrates, amisulpride and fluphenazine were selected for in‐vivo drug‐drug interaction studies in rats to demonstrate the in‐vivo relevance of the in‐vitro findings. Compounds were administered by intraperitoneal injection either alone or in combination with 50 mg kg−1 ciclosporin. The concentration versus time profiles for both drugs were followed in serum as well as in brain tissues. Significant differences between the treatments with the antipsychotic alone versus the combination of antipsychotic with ciclosporin were found for amisulpride. The distribution of amisulpride to the brain was increased and systemic serum levels were likewise increased indicating decreased systemic clearance for the combination regimen. For fluphenazine, systemic levels with and without co‐administraton of ciclosporin were comparable while higher brain‐to‐serum concentration ratios were found after co‐administration of ciclosporin. The findings are explained on the basis of the limited contribution of P‐gp‐mediated transport to the elimination of fluphenazine and to a direct effect with respect to its distribution into the brain.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Abstract
We present a generically applicable approach to determine an extensive set of size-dependent critical quality attributes inside nanoparticulate pharmaceutical products. By coupling ...asymmetrical-flow field-flow fractionation (AF4) measurements directly in-line with solution small angle X-ray scattering (SAXS), vital information such as (i) quantitative, absolute size distribution profiles, (ii) drug loading, (iii) size-dependent internal structures, and (iv) quantitative information on free drug is obtained. Here the validity of the method was demonstrated by characterizing complex mRNA-based lipid nanoparticle products. The approach is particularly applicable to particles in the size range of 100 nm and below, which is highly relevant for pharmaceutical products—both biologics and nanoparticles. The method can be applied as well in other fields, including structural biology and environmental sciences.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
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