Next-Generation EU DataGrid Data Management Services

We describe the architecture and initial implementation of the next-generation of Grid Data Management Middleware in the EU DataGrid (EDG) project. The new architecture stems out of our experience and the users requirements gathered during the two years of running our initial set of Grid Data Management Services. All of our new services are based on the Web Service technology paradigm, very much in line with the emerging Open Grid Services Architecture (OGSA). We have modularized our components and invested a great amount of effort towards a secure, extensible and robust service, starting from the design but also using a streamlined build and testing framework. Our service components are: Replica Location Service, Replica Metadata Service, Replica Optimization Service, Replica Subscription and high-level replica management. The service security infrastructure is fully GSI-enabled, hence compatible with the existing Globus Toolkit 2-based services; moreover, it allows for fine-grained authorization mechanisms that can be adjusted depending on the service semantics.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla,Ca, USA, March 2003 8 pages, LaTeX, the file contains all LaTeX sources - figures are in the directory "figures

The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways

Human fungal pathogens like Candida albicans respond to host immune surveillance by rapidly adapting their transcriptional programs. Chromatin assembly factors are involved in the regulation of stress genes by modulating the histone density at these loci. Here, we report a novel role for the chromatin assembly-associated histone acetyltransferase complex NuB4 in regulating oxidative stress resistance, antifungal drug tolerance and virulence in C. albicans. Strikingly, depletion of the NuB4 catalytic subunit, the histone acetyltransferase Hat1, markedly increases resistance to oxidative stress and tolerance to azole antifungals. Hydrogen peroxide resistance in cells lacking Hat1 results from higher induction rates of oxidative stress gene expression, accompanied by reduced histone density as well as subsequent increased RNA polymerase recruitment. Furthermore, hat1Delta/Delta cells, despite showing growth defects in vitro, display reduced susceptibility to reactive oxygen-mediated killing by innate immune cells. Thus, clearance from infected mice is delayed although cells lacking Hat1 are severely compromised in killing the host. Interestingly, increased oxidative stress resistance and azole tolerance are phenocopied by the loss of histone chaperone complexes CAF-1 and HIR, respectively, suggesting a central role for NuB4 in the delivery of histones destined for chromatin assembly via distinct pathways. Remarkably, the oxidative stress phenotype of hat1Delta/Delta cells is a species-specific trait only found in C. albicans and members of the CTG clade. The reduced azole susceptibility appears to be conserved in a wider range of fungi. Thus, our work demonstrates how highly conserved chromatin assembly pathways can acquire new functions in pathogenic fungi during coevolution with the host

Bridging clinical information systems and grid middleware: a Medical Data Manager

International audienceThis paper describes the effort to deploy a Medical Data Management service on top of the EGEE grid infrastructure. The most widely accepted medical image stan- dard, DICOM, was developed for fulfilling clinical practice. It is implemented in most medical image acquisition and analysis devices. The EGEE middleware is us- ing the SRM standard for handling grid files. Our prototype is exposing an SRM compliant interface to the grid middleware, transforming on the fly SRM requests into DICOM transactions. The prototype ensures user identification, strict file ac- cess control and data protection through the use of relevant grid services. This Medical Data Manager is easing the access to medical databases needed for many medical data analysis applications deployed today. It offers a high level data man- agement service, compatible with clinical practices, which encourages the migration of medical applications towards grid infrastructures. A limited scale testbed has been deployed as a proof of concept of this new service. The service is expected to be put into production with the next EGEE middleware generation

Artificial Parthenogenesis in Rana Pipiens

This 9 page thesis attempts to prove that development of a frog\u27s egg may be initiated by a mechanical force alone, that this development is materially aided by a chemical agent, and to suggest the possible significance of each step to aid further investigation

A Secure Grid Medical Data Manager Interfaced to the gLite Middleware

International audienceThe medical community is producing and manipulating a tremendous volume of digital data for which computerized archiving, processing and analysis is needed. Grid infrastructures are promising for dealing with challenges arising in computerized medicine but the manipulation of medical data on such infrastructures faces both the problem of interconnecting medical information systems to Grid middlewares and of preserving patients' privacy in a wide and distributed multi-user system. These constraints are often limiting the use of Grids for manipulating sensitive medical data. This paper describes our design of a medical data management system taking advantage of the advanced gLite data management services, developed in the context of the EGEE project, to fulfill the stringent needs of the medical community. It ensures medical data protection through strict data access control, anonymization and encryption. The multi-level access control provides the flexibility needed for imple! menting complex medical use-cases. Data anonymization prevents the exposure of most sensitive data to unauthorized users, and data encryption guarantees data protection even when it is stored at remote sites. Moreover, the developed prototype provides a Grid storage resource manager (SRM) interface to standard medical DICOM servers thereby enabling transparent access to medical data without interfering with medical practice

Cellular responses of Candida albicans to phagocytosis and the extracellular activities of neutrophils are critical to counteract carbohydrate starvation, oxidative and nitrosative stress

Acknowledgments We thank Alexander Johnson (yhb1D/D), Karl Kuchler (sodD/D mutants), Janet Quinn (hog1D/D, hog1/cap1D/D, trx1D/D) and Peter Staib (ssu1D/D) for providing mutant strains. We acknowledge helpful discussions with our colleagues from the Microbial Pathogenicity Mechanisms Department, Fungal Septomics and the Microbial Biochemistry and Physiology Research Group at the Hans Kno¨ll Institute (HKI), specially Ilse D. Jacobsen, Duncan Wilson, Sascha Brunke, Lydia Kasper, Franziska Gerwien, Sea´na Duggan, Katrin Haupt, Kerstin Hu¨nniger, and Matthias Brock, as well as from our partners in the FINSysB Network. Author Contributions Conceived and designed the experiments: PM HW IMB AJPB OK BH. Performed the experiments: PM CD HW. Analyzed the data: PM HW IMB AJPB OK BH. Wrote the paper: PM HW OK AJPB BH.Peer reviewedPublisher PD

Cold flow modelling of dual fluidised bed pyrolysis

High temperature pyrolysis at about 600-700°C of carbon containing waste materials (plastic waste, shredded old tires, biogenic residues, etc.) is an attractive technology for substitution of fossil fuels in industrial processes. A dual fluidized bed system is investigated in a scaled cold flow model. This model consists of a riser as combustion section and a bubbling fluidized bed as pyrolysis section. The pyrolysis section is aimed to convert the solid feed material into pyrolysis oil as well as permanent gas components. This gas stream can be directly used e.g. in rotary kilns at temperatures of 400-600°C with high tar content and therefore high heating value. The char is transported with the bed material to the riser to provide the energy for the pyrolysis, transported via the hot bed material. Moreover, the pyrolysing section will be used to separate unconvertable materials such as metal pieces, stones, etc. from the process. For certain feed materials the pyrolysing section could be built as circulating fluidized bed to perform a classification of the feed material. Thus different residence time in the pyrolyser can be achieved, depending on the fuel particle size and fluidization. The results are displayed inside a regime map of gas-solid fluidized beds. Bed material residence times as well as residence times of model particles of the feedstock are given. The investigations lead to a design of a system to be applicable for various feedstock materials as input for industrial processes

Cold flow modelling of dual fluidised bed pyrolysi

High temperature pyrolysis at about 600-700°C of carbon containing waste materials (plastic waste, shredded old tires, biogenic residues, etc.) is an attractive technology for substitution of fossil fuels in industrial processes. A dual fluidized bed system is investigated in a scaled cold flow model. This model consists of a riser as combustion section and a bubbling fluidized bed as pyrolysis section. The pyrolysis section is aimed to convert the solid feed material into pyrolysis oil as well as permanent gas components. This gas stream can be directly used e.g. in rotary kilns at temperatures of 400-600°C with high tar content and therefore high heating value. The char is transported with the bed material to the riser to provide the energy for the pyrolysis, transported via the hot bed material. Moreover, the pyrolysing section will be used to separate unconvertable materials such as metal pieces, stones, etc. from the process. For certain feed materials the pyrolysing section could be built as circulating fluidized bed to perform a classification of the feed material. Thus different residence time in the pyrolyser can be achieved, depending on the fuel particle size and fluidization. The results are displayed inside a regime map of gas-solid fluidized beds. Bed material residence times as well as residence times of model particles of the feedstock are given. The investigations lead to a design of a system to be applicable for various feedstock materials as input for industrial processes

Code Generation from UML Models

Creating a generic, object-oriented, component-based, transactional business system, which covers the whole lifecycle, is possible only with the integration of commercial tools, component technologies, newly developed class libraries and by using code generators. Most of the recently used tools for development techniques are focusing on only one of the layers of the model from the code generation point of view. As a consequence, the inter-layer connections are lost in the generated code. In this article, we describe a code generator technique which uses a UML model as a starting point and generates several layers directly. While generating the code, it preserves the original interlayer relationships originated in the model. Based on our experiences with 4GL systems it is obvious that there is a need to provide customisation in the generated code. We offer a multi-paradigm approach [1] to let the developer choose the appropriate solution for her or his implementation

Novel insights into host-fungal pathogen interactions derived from live-cell imaging

Acknowledgments The authors acknowledge funding from the Wellcome Trust (080088, 086827, 075470 and 099215) including a Wellcome Trust Strategic Award for Medical Mycology and Fungal Immunology 097377 and FP7-2007–2013 grant agreement HEALTH-F2-2010-260338–ALLFUN to NARG.Peer reviewedPublisher PD