The Design of a High-Integrity Disk Management Subsystem

This dissertation describes and experimentally evaluates the design of the Logical Disk, a disk management subsystem that guarantees the integrity of data stored on disk even after system failures, while still providing performance competitive to other storage systems. Current storage systems that use the hard disk as storage medium, such as file systems, often do not provide sufficient protection against loss of data after a system failure. The designers of such systems are afraid that the amount of effort necessary for data protection would also result in too much loss of performance. The Logical Disk uses many different techniques to guarantee data integrity, including the support to execute multiple commands as one atomic action and avoiding `in-place updates' at all times. The techniques used to provide competitive performance include the technique of combining many, small write commands into one large, sequential, and thus efficient, write to disk, and clustering the data on disk continuously and automatically.Tanenbaum, A.S. [Promotor]Jonge, W. de [Copromotor

Design of a Secure and Decentralized Location Service for Agent Platforms

Abstract. Agent platforms designed for Internet-scale, open networks need scalable and secure location services for agents and services. The location service based on the Fonkey public key distribution infrastructure presented in this paper has been designed and implemented for this purpose. It is scalable in the total number of published identifier–contact address pairs, the number of updates/changes, and the number of agent platforms publishing and requesting contact addresses. This system also supports a signing mechanism to authenticate the publisher of an identifier–contact address pair. Experimental results show that the current implementation based on the Bunshin/Free Pastry overlay network exhibits good scaling behavior.

SamenMarkt®, a Proposal for Restoring Trust in the Horticultural Fresh Food Market by Using Multi-Agent System Technology

In the horticultural fresh food supply chain network in the Netherlands, a crisis is emerging. The market is out of balance and many growers are facing bankruptcy, in the period of 2011–2013, 50% of the growers were not able to pay interest and redemption. Trust between participants in the supply chain network has decreased. This chapter presents the currently not established and identifies design requirements for new systems to address this challenge and provide directions for possible improvement. As a result, this chapter introduces the concept of SamenMarkt®, a participatory system in which multi-agent system technology enables distributed price negotiation, distribution and communication between producers, retailers and consumers. A SWOT analysis of the concept of SamenMarkt® is provided together with a research and development plan in which simulation and emulation create the basis for stakeholder- and participant involvement in the design process of a distributed digital market place. Further research aims to study how SamenMarkt® can provide a solution space for the emerging global food crises. At present, we are using agent-based modelling to simulate the present market and scenarios. The next step will be to build the actual agent-based platform for real-time negotiations and business intelligence

The role of MORC3 in silencing transposable elements in mouse embryonic stem cells

Background Microrchidia proteins (MORCs) are involved in epigenetic gene silencing in a variety of eukaryotic organisms. Deletion of MORCs result in several developmental abnormalities and their dysregulation has been implicated in developmental disease and multiple cancers. Specifically, mammalian MORC3 mutations are associated with immune system defects and human cancers such as bladder, uterine, stomach, lung, and diffuse large B cell lymphomas. While previous studies have shown that MORC3 binds to H3K4me3 in vitro and overlaps with H3K4me3 ChIP-seq peaks in mouse embryonic stem cells, the mechanism by which MORC3 regulates gene expression is unknown. Results In this study, we identified that mutation in Morc3 results in a suppressor of variegation phenotype in a Modifiers of murine metastable epialleles Dominant (MommeD) screen. We also find that MORC3 functions as an epigenetic silencer of transposable elements (TEs) in mouse embryonic stem cells (mESCs). Loss of Morc3 results in upregulation of TEs, specifically those belonging to the LTR class of retrotransposons also referred to as endogenous retroviruses (ERVs). Using ChIP-seq we found that MORC3, in addition to its known localization at H3K4me3 sites, also binds to ERVs, suggesting a direct role in regulating their expression. Previous studies have shown that these ERVs are marked by the repressive histone mark H3K9me3 which plays a key role in their silencing. However, we found that levels of H3K9me3 showed only minor losses in Morc3 mutant mES cells. Instead, we found that loss of Morc3 resulted in increased chromatin accessibility at ERVs as measured by ATAC-seq. Conclusions Our results reveal MORC3 as a novel regulator of ERV silencing in mouse embryonic stem cells. The relatively minor changes of H3K9me3 in the Morc3 mutant suggests that MORC3 acts mainly downstream of, or in a parallel pathway with, the TRIM28/SETDB1 complex that deposits H3K9me3 at these loci. The increased chromatin accessibility of ERVs in the Morc3 mutant suggests that MORC3 may act at the level of chromatin compaction to effect TE silencing.Molecular Technology and Informatics for Personalised Medicine and Healt

Vortex merger near a topographic slope in a homogeneous rotating fluid

This work is a contribution to the PHYSINDIEN research program. It was supported by CNRS-RFBR contract PRC 1069/16-55-150001.The effect of a bottom slope on the merger of two identical Rankine vortices is investigated in a two dimensional, quasi-geostrophic, incompressible fluid. When two cyclones initially lie parallel to the slope, and more than two vortex diameters away from the slope, the critical merger distance is unchanged. When the cyclones are closer to the slope, they can merge at larger distances, but they lose more mass into filaments, thus weakening the efficiency of merger. Several effects account for this: the topographic Rossby wave advects the cyclones, reduces their mutual distance and deforms them. This along shelf wave breaks into filaments and into secondary vortices which shear out the initial cyclones. The global motion of fluid towards the shallow domain and the erosion of the two cyclones are confirmed by the evolution of particles seeded both in the cyclone sand near the topographic slope. The addition of tracer to the flow indicates that diffusion is ballistic at early times. For two anticyclones, merger is also facilitated because one vortex is ejected offshore towards the other, via coupling with a topographic cyclone. Again two anticyclones can merge at large distance but they are eroded in the process. Finally, for taller topographies, the critical merger distance is again increased and the topographic influence can scatter or completely erode one of the two initial cyclones. Conclusions are drawn on possible improvements of the model configuration for an application to the ocean.PostprintPeer reviewe