Data production models for the CDF experiment

The data production for the CDF experiment is conducted on a large Linux PC farm designed to meet the needs of data collection at a maximum rate of 40 MByte/sec. We present two data production models that exploits advances in computing and communication technology. The first production farm is a centralized system that has achieved a stable data processing rate of approximately 2 TByte per day. The recently upgraded farm is migrated to the SAM (Sequential Access to data via Metadata) data handling system. The software and hardware of the CDF production farms has been successful in providing large computing and data throughput capacity to the experiment.Comment: 8 pages, 9 figures; presented at HPC Asia2005, Beijing, China, Nov 30 - Dec 3, 200

Data processing model for the CDF experiment

The data processing model for the CDF experiment is described. Data processing reconstructs events from parallel data streams taken with different combinations of physics event triggers and further splits the events into datasets of specialized physics datasets. The design of the processing control system faces strict requirements on bookkeeping records, which trace the status of data files and event contents during processing and storage. The computing architecture was updated to meet the mass data flow of the Run II data collection, recently upgraded to a maximum rate of 40 MByte/sec. The data processing facility consists of a large cluster of Linux computers with data movement managed by the CDF data handling system to a multi-petaByte Enstore tape library. The latest processing cycle has achieved a stable speed of 35 MByte/sec (3 TByte/day). It can be readily scaled by increasing CPU and data-handling capacity as required.Comment: 12 pages, 10 figures, submitted to IEEE-TN

Current polarity-dependent manipulation of antiferromagnetic domains

Antiferromagnets have several favourable properties as active elements in spintronic devices, including ultra-fast dynamics, zero stray fields and insensitivity to external magnetic fields. Tetragonal CuMnAs is a testbed system in which the antiferromagnetic order parameter can be switched reversibly at ambient conditions using electrical currents. In previous experiments, orthogonal in-plane current pulses were used to induce 90° rotations of antiferromagnetic domains and demonstrate the operation of all-electrical memory bits in a multi-terminal geometry. Here, we demonstrate that antiferromagnetic domain walls can be manipulated to realize stable and reproducible domain changes using only two electrical contacts. This is achieved by using the polarity of the current to switch the sign of the current-induced effective field acting on the antiferromagnetic sublattices. The resulting reversible domain and domain wall reconfigurations are imaged using X-ray magnetic linear dichroism microscopy, and can also be detected electrically. Switching by domain-wall motion can occur at much lower current densities than those needed for coherent domain switching

Extremely stable graphene electrodes doped with macromolecular acid

Although conventional p-type doping using small molecules on graphene decreases its sheet resistance (Rsh), it increases after exposure to ambient conditions, and this problem has been considered as the biggest impediment to practical application of graphene electrodes. Here, we report an extremely stable graphene electrode doped with macromolecular acid (perfluorinated polymeric sulfonic acid (PFSA)) as a p-type dopant. The PFSA doping on graphene provides not only ultra-high ambient stability for a very long time (> 64 days) but also high chemical/thermal stability, which have been unattainable by doping with conventional small-molecules. PFSA doping also greatly increases the surface potential (similar to 0.8 eV) of graphene, and reduces its Rsh by similar to 56%, which is very important for practical applications. High-efficiency phosphorescent organic light-emitting diodes are fabricated with the PFSA-doped graphene anode (similar to 98.5 cd A(-1) without out-coupling structures). This work lays a solid platform for practical application of thermally-/chemically-/air-stable graphene electrodes in various optoelectronic devices

Functional genomic screening identifies dual leucine zipper kinase as a key mediator of retinal ganglion cell death

Glaucoma, a major cause of blindness worldwide, is a neurodegenerative optic neuropathy in which vision loss is caused by loss of retinal ganglion cells (RGCs). To better define the pathways mediating RGC death and identify targets for the development of neuroprotective drugs, we developed a high-throughput RNA interference screen with primary RGCs and used it to screen the full mouse kinome. The screen identified dual leucine zipper kinase (DLK) as a key neuroprotective target in RGCs. In cultured RGCs, DLK signaling is both necessary and sufficient for cell death. DLK undergoes robust posttranscriptional up-regulation in response to axonal injury in vitro and in vivo. Using a conditional knockout approach, we confirmed that DLK is required for RGC JNK activation and cell death in a rodent model of optic neuropathy. In addition, tozasertib, a small molecule protein kinase inhibitor with activity against DLK, protects RGCs from cell death in rodent glaucoma and traumatic optic neuropathy models. Together, our results establish a previously undescribed drug/drug target combination in glaucoma, identify an early marker of RGC injury, and provide a starting point for the development of more specific neuroprotective DLK inhibitors for the treatment of glaucoma, nonglaucomatous forms of optic neuropathy, and perhaps other CNS neurodegenerations

Predicting the protein-protein interactions using primary structures with predicted protein surface

<p>Abstract</p> <p>Background</p> <p>Many biological functions involve various protein-protein interactions (PPIs). Elucidating such interactions is crucial for understanding general principles of cellular systems. Previous studies have shown the potential of predicting PPIs based on only sequence information. Compared to approaches that require other auxiliary information, these sequence-based approaches can be applied to a broader range of applications.</p> <p>Results</p> <p>This study presents a novel sequence-based method based on the assumption that protein-protein interactions are more related to amino acids at the surface than those at the core. The present method considers surface information and maintains the advantage of relying on only sequence data by including an accessible surface area (ASA) predictor recently proposed by the authors. This study also reports the experiments conducted to evaluate a) the performance of PPI prediction achieved by including the predicted surface and b) the quality of the predicted surface in comparison with the surface obtained from structures. The experimental results show that surface information helps to predict interacting protein pairs. Furthermore, the prediction performance achieved by using the surface estimated with the ASA predictor is close to that using the surface obtained from protein structures.</p> <p>Conclusion</p> <p>This work presents a sequence-based method that takes into account surface information for predicting PPIs. The proposed procedure of surface identification improves the prediction performance with an <it>F-measure </it>of 5.1%. The extracted surfaces are also valuable in other biomedical applications that require similar information.</p

Virologie / Bakteriologie / Mykologie

141 - Effizienz von Kaliumhypochlorit zur Inaktivierung ausgewählter pilzlicher, bakterieller und viraler PflanzenkrankheitserregerEfficancy of Potassium Hypochlorite (KClO) to inactivate selected plant pathogenic fungi, bacteria and virusesMarlon-Hans Rodríguez, Martina Bandte, Gerhard Fischer, Carmen Büttner142 - Eignung von elektrolytisch generiertem Kaliumhypochlorit zur Inaktivierung von Pflanzenviren in rezirkulierender Nährlösungen im Gewächshausanbau von TomatenAbility of electrolysed produced Potassium Hypochlorite (KClO) to inactivate plant viruses in recirculating nutrient solutions in greenhouse production of tomatosJanine Paulke, Martina Bandte, Carmen Büttner143 - Ultrafiltration und Ultrazentrifugation zur Konzentrierung von Pflanzenviren in NährlösungUltrafiltration and ultracentrifugation as tools to concentrate plant viruses in nutrient solutionJanina Vincenz, Martina Bandte, Carmen Büttner144 - Reinigung doppelsträngiger RNA in Verbindung mit Hochdurchsatzsequenzierung als Werkzeug zum Nachweis von RNA Viren in PflanzenThe combination of double-stranded RNA isolation and deep sequencing as an unspecific diagnostic tool to assess the presence of RNA viruses in plantsTill Lesker, Paul Rentz, Edgar Maiss145 - Impact of silica supplementation on virus infected cucumber culturesRolle der Kieselsäureapplikation Virus infizierter GurkenkulturenSabine Holz, Grzegorz Bartoszewski , Michael Kube, Carmen Büttner146 - Untersuchungen zum Auftreten des Arabis mosaic virus in Birken aus Rovaniemi (Finnland) mit Virus-spezifischen SymptomenInvestigations on the occurence of Arabis mosaic virus in birches from Rovaniemi (Finland) with virus-specific symptomsRichard Pauwels, Markus Rott, Susanne von Bargen, Carmen Büttner147 - Cherry leaf roll virus in Betula spp. in Finland: what do we know about its population diversity?Cherry leaf roll virus in Birken-Arten in Finnland: Was wissen wir über die Populationsdiversität?A. Rumbou, S. von Bargen, M. Rott, R. Jalkanen, C. Büttner148 - Viruserkrankungen im WeinbauViroses in viticultureHenriette Gruber, Patricia Bohnert, Christiane Rieger149 - Molecular analysis of Tobacco rattle virus isolates from potatoes in various parts of GermanyKerstin Lindner, Renate Koenig150 - Detektion und Diversität des European mountain ash ringspot-associated virus (EMARaV) in Ebereschen (Sorbus aucuparia L.) in NorwegenDetection and variability of European mountain ash ringspot-associated virus (EMARaV) in Sorbus aucuparia L. in NorwayTheresa Büttner, Jenny Robel, Hans-Peter Mühlbach, Susanne von Bargen, Carmen Büttner151 - Charakterisierung des European mountain ash ringspot-associated virus (EMARaV) in Mehlbeerenarten (Sorbus spp.)Characterization of the European mountain ash ringspot-associated virus (EMARaV) in whitebeam species (Sorbus spp.)Luisa Dieckmann, Jenny Robel, Susanne von Bargen, Carmen Büttner152 - Vollständige Genomsequenz eines Carrot virus S Isolates aus Meerfenchel aus SpanienW. Menzel, P. Menzel, S. Winter153 - Nachweis und vollständige Sequenzierung eines Carla- und eines Potex-virus aus Epiphyullum spec.Detection and complete sequence of a Carla- and Potexvirus in Epiphyllum spec.Edgar Maiss, Paul Rentz, Annette Hohe, Rosa Herbst154 - Analysis of mixed populations of latent viruses of apple and rubbery wood disease of apple using new generation sequencingAnalyse von Mischpopulationen latenter Apfelviren und der Gummiholzkrankheit an Apfel mittels HochdurchsatzsequenzierungVladimir Jakovljevic, Patricia Otten, Jonathon Blake, Wilhelm Jelkmann155 - Experiments on transmission of viroids under glass and longevity of viroid RNA in detached leaves under different storage conditionsThi Thu Vo, Heinz-Wilhelm Dehne, Stephan Winter, Joachim Hamacher156 - Phytoplasmen in Schleswig-HolsteinPhytoplasmas in the state of Schleswig-HolsteinG. Henkel, C. Willmer, M. Wunderlich, B. Golecki157 . Phytoplasmen verändern das Dufststoffbouquet ihres pflanzlichen LebensraumsPlant volatile emission is affected by phytoplasma infectionMargit Rid, Kai Lukat, Svenja Hoferer, Jürgen Gross159 - Ist das Wurzelbild ein Sortierungsmerkmal für durch Candidatus Phytoplasma pyri verursachten Birnenverfall?Is the root file a sorting feature for Pear decline caused by Canditatus Phytoplama pyri?Georg Henkel, Claudia Willmer, Bernd Kaland, Bettina Golecki160 - Die Bedeutung von β-Caryophyllen als Lockstoff für die Apfeltriebsucht übertragende Blattsaugerart Cacopsylla pictaThe impact of β-caryophyllene as attractant for the Apple Proliferation transmitting insect Cacopsylla pictaConstanze Mesca, Svenja Hoferer, Jürgen Gross161 - Echte Mehltauarten an Beet- und BalkonpflanzenSpecies of powdery mildews on bedding plantsUlrike Brielmaier-Liebetanz162 - Echter Mehltau an Petersilie – Untersuchungen zum WirtspflanzenspektrumPowdery Mildew of Parsley – studies on the host rangePeggy Marx, Ute Gärber163 - Falscher Mehltau an Petersilie – Untersuchungen zum Wirtspflanzenspektrum und molekularbiologische CharakterisierungDowny mildew of parsley – studies on the host range and molecular characterizationGabriele Leinhos, Hermann-Josef Krauthausen, Frank Brändle164 - Welkekrankheit an Euonymus japonicaWilt disease on Euonymus japonicaUlrike Brielmaier-Liebetanz, Roswitha Ulrich, Stefan Wagner, Sabine Werres165 - Taxonomische Analyse der mikrobiellen Gemeinschaft von Zuckerrüben unter unterschiedlichen Lagerbedingungen mittels Hochdurchsatz-Amplikonsequenzierung von unterschiedlichen MarkergenenTaxonomic analysis of the microbial community in stored sugar beets using highthroughput sequencing of different marker genesSebastian Liebe, Daniel Wibberg, Anika Winkler, Alfred Pühler, Andreas Schlüter, Mark Varrelmann166 - Molecular characterization of a novel mycovirus found in Rhizoctonia solani AG 2-2IIIBMolekulare Charakterisierung eines neuen Mycovirus aus Rhizoctonia solani AG 2-2 IIIBAnika Bartholomäus, Mark Varrelman