ASCIIGenome: a command line genome browser for console terminals.

PubMed

Beraldi, Dario

2017-05-15

Current genome browsers are designed to work via graphical user interfaces (GUIs), which, however intuitive, are not amenable to operate within console terminals and therefore are difficult to streamline or integrate in scripts. To circumvent these limitations, ASCIIGenome runs exclusively via command line interface to display genomic data directly in a terminal window. By following the same philosophy of UNIX tools, ASCIIGenome aims to be easily integrated with the command line, including batch processing of data, and therefore enables an effective exploration of the data. ASCIIGenome is written in Java. Consequently, it is a cross-platform tool and requires minimal or no installation. Some of the common genomic data types are supported and data access on remote ftp servers is possible. Speed and memory footprint are comparable to or better than those of common genome browsers. Software and source code (MIT License) are available at https://github.com/dariober/ASCIIGenome with detailed documentation at http://asciigenome.readthedocs.io . Dario.beraldi@cruk.cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Binding energy of e^+Li using the Peach model potential.

NASA Astrophysics Data System (ADS)

Shertzer, Janine; Ward, Sandra

2006-05-01

The l-independent, parametric model potential developed by Peach^1 for describing the electron interaction with the alkali ion core yields energy levels that are in excellent agreement with experiment. Because of its relative simplicity, this model potential is an attractive choice for studying e^+- Li collisions;^2,3 the e^+-ion core interaction is obtained by changing the sign of the static term in the interaction. In order to test the usefulness of the potential for describing the physics of an effective three-body system, we calculated the binding energy of e^+Li. This is a stringent test, because the system is very weakly bound. Our results are in excellent agreement with previous calculations,^4 including those using the exact four-body Hamiltonian.^5 This work was funded by NSF under collaborative Grant PHYS-0440714 (JS) and PHYS-0440565 (SJW). ^1G. Peach, H.E. Saraph and M.J. Seaton, J. Phys. B 21, 3669 (1988). ^2M.S.T. Watts and J.W. Humberston, J. Phys. B 25, L491 (1992). ^3S. J. Ward and J. Shertzer, Phys. Rev. A 68, 032720 (2003). ^4J. Mitroy, M.W.J. Bromley, and G.G. Ryzhikh, J. Phys. B 35, R81 (2002). ^5Massimo Mella, Gabriele Morosi, and Dario Bressanini, J. Chem. Phys. 111, 108 (1999).

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods.

PubMed

Schaffter, Thomas; Marbach, Daniel; Floreano, Dario

2011-08-15

Over the last decade, numerous methods have been developed for inference of regulatory networks from gene expression data. However, accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate benchmarks and the lack of tools for a differentiated analysis of network predictions on such benchmarks. Here, we describe a novel and comprehensive method for in silico benchmark generation and performance profiling of network inference methods available to the community as an open-source software called GeneNetWeaver (GNW). In addition to the generation of detailed dynamical models of gene regulatory networks to be used as benchmarks, GNW provides a network motif analysis that reveals systematic prediction errors, thereby indicating potential ways of improving inference methods. The accuracy of network inference methods is evaluated using standard metrics such as precision-recall and receiver operating characteristic curves. We show how GNW can be used to assess the performance and identify the strengths and weaknesses of six inference methods. Furthermore, we used GNW to provide the international Dialogue for Reverse Engineering Assessments and Methods (DREAM) competition with three network inference challenges (DREAM3, DREAM4 and DREAM5). GNW is available at http://gnw.sourceforge.net along with its Java source code, user manual and supporting data. Supplementary data are available at Bioinformatics online. dario.floreano@epfl.ch.

Cold plasma treatment in wound care: efficacy and risk assessment

NASA Astrophysics Data System (ADS)

Stoffels, Eva

2007-10-01

Cold atmospheric plasma is an ideal medium for non-destructive modification of vulnerable surfaces. One of the most promising medical applications of cold plasma treatment is wound healing. Potential advantages in wound healing have been demonstrated in vitro: the plasma does not necrotize the cells and does not affect the extracellular matrix [1], has clear bactericidal or bacteriostatic effects [2], and stimulates fibroblast cells towards faster attachment and proliferation [3]. However, safety issues, such as the potential cytotoxicity of the plasma must be clarified prior to clinical implementation. This work comprises the recent facts on sub-lethal plasma effects on mammalian cells, as well as studies on apoptosis induction and quantitative assessment of DNA damage. Fibroblast, smooth muscle and endothelial cells were treated using the standard cold plasma needle [1,2]; intra- and extracellular oxidant levels as well as the influence of the plasma on intracellular antioxidant balance were monitored using appropriate fluorescent markers [1]. We have studied long-term cellular damage was monitored using flow cytometry to determine the DNA profiles in treated cells. Dose-response curves were obtained: increased proliferation as well as apoptosis were visualized under different treatment conditions. The results from the in vitro studies are satisfying. [1] I.E. Kieft, ``Plasma needle: exploring biomedical applications of non-thermal plasmas'', PhD Thesis, Eindhoven University of Technology (2005). [2] R.E.J. Sladek, ``Plasma needle: non-thermal atmospheric plasmas in dentistry'' PhD Thesis, Eindhoven University of Technology (2006). [3] I.E. Kieft, D. Darios, A.J.M. Roks, E. Stoffels, IEEE Trans. Plasma Sci. 34(4), 2006, pp. 1331-1336.

A study on flash sintering and related phenomena in titania and its composite with alumina

NASA Astrophysics Data System (ADS)

Shikhar

In 2010, Cologna et. al. [1] reported that with a help of small electric field 120 Vcm-1, the sintering temperature of 3 mol % yittria stabilized zirconia could be brought down to 850°C from 1450°C. On top of reducing the temperature requirements, the green sample could be sintered from starting density of 50% to near full density in mere 5 seconds, a sintering rate three orders of magnitude higher than conventional methods. This discovery led to the emergence of a new field of enhanced sintering with electric field, named "Flash Sintering". The objective of this thesis is to understand the phenomenological behavior of flash-sintering and related phenomena on titania and its composites with alumina at elevated temperature. The possible mechanisms to explain flash sintering are discussed: Joule heating and the avalanche of defect generation [2], both induced by the rapid rise in conductivity just before the onset of the flash. Apparently, both mechanisms play a role. The thesis covers the response of pure titania and composites of titania-alumina under flash and compared with conventional sintering. We start with the sintering behavior of pure titania and observe lowering of sintering temperature requirements with higher applied electric field. The conductivity of titania during flash is also measured, and compared with the nominal conductivity of titania at equivalent temperatures. The conductivity during flash is determined to be have a different activation energy. For the composites of titania-alumina, effect of flash on the constrained sintering was studied. It is a known fact that sintering of one component of composite slows down when the other component of a different densification rate is added to it, called constrained sintering. In our case, large inclusions of alumina particles were added to nano-grained titania green compact that hindered its densification. Flash sintering was found to be overcoming this problem and near full densification was achieved

MO-FG-CAMPUS-TeP3-01: A Model of Baseline Shift to Improve Robustness of Proton Therapy Treatments of Moving Tumors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Souris, K; Barragan Montero, A; Di Perri, D

Purpose: The shift in mean position of a moving tumor also known as “baseline shift”, has been modeled, in order to automatically generate uncertainty scenarios for the assessment and robust optimization of proton therapy treatments in lung cancer. Methods: An average CT scan and a Mid-Position CT scan (MidPCT) of the patient at the planning time are first generated from a 4D-CT data. The mean position of the tumor along the breathing cycle is represented by the GTV contour in the MidPCT. Several studies reported both systematic and random variations of the mean tumor position from fraction to fraction. Ourmore » model can simulate this baseline shift by generating a local deformation field that moves the tumor on all phases of the 4D-CT, without creating any non-physical artifact. The deformation field is comprised of normal and tangential components with respect to the lung wall in order to allow the tumor to slip within the lung instead of deforming the lung surface. The deformation field is eventually smoothed in order to enforce its continuity. Two 4D-CT series acquired at 1 week of interval were used to validate the model. Results: Based on the first 4D-CT set, the model was able to generate a third 4D-CT that reproduced the 5.8 mm baseline-shift measured in the second 4D-CT. Water equivalent thickness (WET) of the voxels have been computed for the 3 average CTs. The root mean square deviation of the WET in the GTV is 0.34 mm between week 1 and week 2, and 0.08 mm between the simulated data and week 2. Conclusion: Our model can be used to automatically generate uncertainty scenarios for robustness analysis of a proton therapy plan. The generated scenarios can also feed a TPS equipped with a robust optimizer. Kevin Souris, Ana Barragan, and Dario Di Perri are financially supported by Televie Grants from F.R.S.-FNRS.« less

VizieR Online Data Catalog: The Initial Gaia Source List (IGSL) (Smart, 2013)

NASA Astrophysics Data System (ADS)

Smart, R. L.; Nicastro, L.

2013-11-01

The IGSL is a compilation catalog produced for the Gaia mission. We have combined data from the following catalogs or datasets to produce a homogenous list of positons, proper motions, photometry in a blue and red band and estimates of the magnitudes in the Gaia G and G_RVS bands. Included Catalogs: Tycho2, LQRF, UCAC4, SDSS-DR9, PPMXL, GSC23, GEPC, OGLE, Sky2000, 2MASS. Note that in compiling the various entries we did not consider the individual flags. Overall, we think this catalog is reliable but there will be errors, mismatches and duplicates. The user should use this catalog with that in mind, it is fine for statistical studies that has some way to remove obviously incorrect entries but it should only be used with care for individual objects. The source catalogs used to produce the IGSL are: * The Gaia Ecliptic Pole Catalog, version 3.0 (GEPC) Altmann & Bastian 2009, "Ecliptic Poles Catalogue Version 1.1" ESA Document GAIA-C3-TN-ARI-MA-002 URL http://www.rssd.esa.int/llink/livelink/open/2885828 * GSC2.3: GSC2 version 2.3, Lasker et al. 2008AJ....136..735L (I/305) * an excerpt of the 4th version of the Gaia Initial QSO Catalog (GIQC) as compiled by the GWP-S-335-13000, formed by Alexandre H. Andrei, Christophe Barache, Dario N. da Silva Neto, Francois Taris, Geraldine Bourda, Jean-Francois Le Campion, Jean Souchay, J.J. Pereira Osorio, Julio I. Bueno de Camargo, Marcelo Assafin, Roberto Vieira Martins, Sebastien Bouquillon, Sebastien Lambert, Sonia Anton, Patrick Charlot * OGLE: Optical Gravitational Lensing Experiment version III (Szymaski et al., 2011, Cat. J/AcA/61/83) * PPMXL: Positions and Proper Motions "Extra Large" Catalog, Roeser et al. (2010, Cat. I/317) * SDSS: Sloan Digital Sky Survey data release 9, Cat. V/139 * UCAC4: Zacharias et al., 2012, Cat. I/322 * Tycho-2, Hoeg et al., 2000, Cat. I/259 (1 data file).

Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae)

PubMed Central

Bohlen, Jörg; Šlechtová, Vendula; Altmanová, Marie; Pelikánová, Šárka; Ráb, Petr

2018-01-01

Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei–an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness. The demonstrably monophyletic freshwater loach family Botiidae, branching to evolutionary diploid and tetraploid lineages separated >25 Mya, offers a suited model group for comparing the long-term repetitive DNA evolution. For this, we integrated phylogenetic analyses with cytogenetical survey involving Giemsa- and Chromomycin A3 (CMA3)/DAPI stainings and fluorescence in situ hybridization with 5S/45S rDNA, U2 snDNA and telomeric probes in representative sample of 12 botiid species. The karyotypes of all diploids were composed of 2n = 50 chromosomes, while majority of tetraploids had 2n = 4x = 100, with only subtle interspecific karyotype differences. The exceptional karyotype of Botia dario (2n = 4x = 96) suggested centric fusions behind the 2n reduction. Variable patterns of FISH signals revealed cases of intraspecific polymorphisms, rDNA amplification, variable degree of correspondence with CMA3+ sites and almost no phylogenetic signal. In tetraploids, either additivity or loci gain/loss was recorded. Despite absence of classical interstitial telomeric sites, large blocks of interspersed rDNA/telomeric regions were found in diploids only. We uncovered different molecular drives of studied repetitive DNA classes within botiid genomes as well as the advanced stage of the re-diploidization process in tetraploids. Our results may

A 500-year overview and analysis of flood changes in Europe: preliminary results

NASA Astrophysics Data System (ADS)

Kiss, Andrea

2014-05-01

Long-term flood series can be gained by combining evidence and systematic hydrological observations. Following various already existing local and regional studies, an important aim of the present work is to create a broad European database of long flood chronologies and to use them for detecting changes in flood regimes with respect to common break points. Another aim of the investigations is to reveal the main causes (e.g. atmospheric, human) of these changes and study spatial and temporal variability of floods on a European scale. In the presentation we provide an overview on the current stage of these Europe-wide investigations, including the available source types (i.e. documentary and instrumental), geographical coverage, temporal and spatial distribution of long-term flood series applied in the study. The first research results concerns basic information on magnitude, frequency and seasonality of floods (with special consideration of detectable changes). Full list of authors in alphabetic order: Mariano Barriendos (1), Günter Blöschl (2), Rudolf Brázdil (3), Gerardo Benito (4), Chiara Bertolin (5), Dario Camuffo (5), Gaston Demarée (6), Líbor Elleder (7), Silvi Enzi (8), Rüdiger Glaser (9), Julia Hall (2), Andrea Kiss (2), Oldrich Kotyza (10), Carmen Maria del Llasat (1), Neil MacDonald (11), Rui Perdigao (2), Dag Retsö (12), Lars Roald (13), Josep Luis Ruiz Bellet (1), Johannes Schönbeim (9), Petra Schmocker-Fackel (14), Lothar Schulte (1), Hubert Valasek (15), Oliver Wetter (16) (1) Faculty of Geography and History, University of Barcelona, Spain (2) Institute of Hydrological Engineering and Water Resources Management, TU Wien (3) Institute of Geography, Masaryk University Brno, Czech Republic (4) Laboratory of Hydrology and Geomorphology, Center of Env. Sciences, Madrid, Spain (5) Institute of Atmospheric Sciences and Climate, National Research Council, Rome, Italy (6) Royal Meteorological Institute, Brussels, Belgium (7) Research Group of

Diacylglycerol, phosphatidic acid, and their metabolic enzymes in synaptic vesicle recycling.

PubMed

Tu-Sekine, Becky; Goldschmidt, Hana; Raben, Daniel M

2015-01-01

exocytosis: sphingosine (Camoletto et al., 2009; Chan et al., 2012; Chan and Sieburth, 2012; Darios et al., 2009; Kanno et al., 2010; Rohrbough et al., 2004) and sphingosine-1-phosphate (Chan, Hu, 2012; Chan and Sieburth, 2012; Kanno et al., 2010). Finally a number of reports have focused on the somewhat less well studies roles of sphingolipids and cholesterol in SV cycling. In this report, we review the recent understanding of the roles PLDs, DGKs, and DAG lipases, as well as sphingolipids and cholesterol play in synaptic vesicle cycling. Copyright © 2014. Published by Elsevier Ltd.

Does canopy mean N concentration explain differences in light use efficiency in 14 eddy-covariance sites?

NASA Astrophysics Data System (ADS)

Peltoniemi, Mikko; Pulkkinen, Minna; Kolari, Pasi; Mäkelä, Annikki

2010-05-01

. Mean growing season VPD was the only climatic variable which correlated significantly with the largest actual LUE; none of them correlated with potential LUE. Inclusion of nitrogen in the Prelued-model structure did not improve the goodness of fit of the model. According to our results LUE correlates with mean canopy N concentration. The correlation of mean VPD with the largest actual LUE can also be explained with the model accounting for daily variation in climate, as was made with Prelued-model for the potential LUE. Further studies utilising seasonal values of canopy N are called upon. *Acknowledgements: Eero Nikinmaa, Pertti Hari, Timo Vesala, Tuomas Laurila, Fredrik Lagergren, Meelis Mölder, Anders Lindroth, Thomas Grünwald, Christian Bernhofer, Denis Loustau, Paul Berbigier, Beverly Law, Alison Dunn, Steve Wofsy, Torbjörn Johansson, Torben Christensen, Terry Callaghan, Hans Verbeeck, Remko Duursma, Leonardo Montagnani, Dario Papale, Andreas Ibrom, Ebba Dellwik, Kim Pilegaard, Kentaro Takagi, Eva van Gorsel, Heather Keith, Sonia Wharton, Matthias Falk, Kya Tha Paw U, Matt Schroeder, Jon Lloyd

EDITORIAL: Focus on Dark Matter and Particle Physics

NASA Astrophysics Data System (ADS)

Aprile, Elena; Profumo, Stefano

2009-10-01

Doetinchem, H Gast, T Kirn and S Schael Axion searches with helioscopes and astrophysical signatures for axion(-like) particles K Zioutas, M Tsagri, Y Semertzidis, T Papaevangelou, T Dafni and V Anastassopoulos The indirect search for dark matter with IceCube Francis Halzen and Dan Hooper DIRECT DARK MATTER SEARCHES:EXPERIMENTS Gaseous dark matter detectors G Sciolla and C J Martoff Search for dark matter with CRESST Rafael F Lang and Wolfgang Seidel DIRECT AND INDIRECT PARTICLE DARK MATTER SEARCHES:THEORY Dark matter annihilation around intermediate mass black holes: an update Gianfranco Bertone, Mattia Fornasa, Marco Taoso and Andrew R Zentner Update on the direct detection of dark matter in MSSM models with non-universal Higgs masses John Ellis, Keith A Olive and Pearl Sandick Dark stars: a new study of the first stars in the Universe Katherine Freese, Peter Bodenheimer, Paolo Gondolo and Douglas Spolyar Determining the mass of dark matter particles with direct detection experiments Chung-Lin Shan The detection of subsolar mass dark matter halos Savvas M Koushiappas Neutrino coherent scattering rates at direct dark matter detectors Louis E Strigari Gamma rays from dark matter annihilation in the central region of the Galaxy Pasquale Dario Serpico and Dan Hooper DARK MATTER MODELS The dark matter interpretation of the 511 keV line Céline Boehm Axions as dark matter particles Leanne D Duffy and Karl van Bibber Sterile neutrinos Alexander Kusenko Dark matter candidates Lars Bergström Minimal dark matter: model and results Marco Cirelli and Alessandro Strumia Shedding light on the dark sector with direct WIMP production Partha Konar, Kyoungchul Kong, Konstantin T Matchev and Maxim Perelstein Axinos as dark matter particles Laura Covi and Jihn E Kim

PREFACE: International Conference on Computing in High Energy and Nuclear Physics (CHEP 2010)

NASA Astrophysics Data System (ADS)

Lin, Simon C.; Shen, Stella; Neufeld, Niko; Gutsche, Oliver; Cattaneo, Marco; Fisk, Ian; Panzer-Steindel, Bernd; Di Meglio, Alberto; Lokajicek, Milos

2011-12-01

, as well as two banquets held at the Grand Hotel and Grand Formosa Regent in Taipei. The next CHEP conference will be held in New York, the United States on 21-25 May 2012. We would like to thank the National Science Council of Taiwan, the EU ACEOLE project, commercial sponsors, and the International Advisory Committee and the Programme Committee members for all their support and help. Special thanks to the Programme Committee members for their careful choice of conference contributions and enormous effort in reviewing and editing about 340 post conference proceedings papers. Simon C Lin CHEP 2010 Conference Chair and Proceedings Editor Taipei, Taiwan November 2011 Track Editors/ Programme Committee Chair Simon C Lin, Academia Sinica, Taiwan Online Computing Track Y H Chang, National Central University, Taiwan Harry Cheung, Fermilab, USA Niko Neufeld, CERN, Switzerland Event Processing Track Fabio Cossutti, INFN Trieste, Italy Oliver Gutsche, Fermilab, USA Ryosuke Itoh, KEK, Japan Software Engineering, Data Stores, and Databases Track Marco Cattaneo, CERN, Switzerland Gang Chen, Chinese Academy of Sciences, China Stefan Roiser, CERN, Switzerland Distributed Processing and Analysis Track Kai-Feng Chen, National Taiwan University, Taiwan Ulrik Egede, Imperial College London, UK Ian Fisk, Fermilab, USA Fons Rademakers, CERN, Switzerland Torre Wenaus, BNL, USA Computing Fabrics and Networking Technologies Track Harvey Newman, Caltech, USA Bernd Panzer-Steindel, CERN, Switzerland Antonio Wong, BNL, USA Ian Fisk, Fermilab, USA Niko Neufeld, CERN, Switzerland Grid and Cloud Middleware Track Alberto Di Meglio, CERN, Switzerland Markus Schulz, CERN, Switzerland Collaborative Tools Track Joao Correia Fernandes, CERN, Switzerland Philippe Galvez, Caltech, USA Milos Lokajicek, FZU Prague, Czech Republic International Advisory Committee Chair: Simon C. Lin , Academia Sinica, Taiwan Members: Mohammad Al-Turany , FAIR, Germany Sunanda Banerjee, Fermilab, USA Dario Barberis, CERN

PREFACE: Loops 11: Non-Perturbative / Background Independent Quantum Gravity

NASA Astrophysics Data System (ADS)

Mena Marugán, Guillermo A.; Barbero G, J. Fernando; Garay, Luis J.; Villaseñor, Eduardo J. S.; Olmedo, Javier

2012-05-01

only was it a showroom for the research currently being carried out by many groups throughout the world, but there was also a permanent look towards the future. During these days, the CSIC Campus witnessed many scientific conversations triggered by the interaction amongst the people and groups that participated in LOOPS'11 Madrid and which, in many cases, will crystallise into new results and advances in the field. The conference would not have been possible without the generous help of a number of national and international institutions. The organizers would like to acknowledge the financial support provided by the Spanish Ministry of Science and Innovation (Ministerio de Ciencia e Innovación), the Spanish Research Council, CSIC (Consejo Superior de Investigaciones Cientĺficas), The BBVA Foundation (Fundación BBVA), The CONSOLIDER-CPAN project, the Spanish Society for Gravitation and Relativity (SEGRE), The Universidad Carlos III of Madrid (UC3M), and the European Science Foundation (ESF). The ESF, through the Quantum Gravity and Quantum Geometry network, provided full support for a number of young participants that have contributed to these proceedings: Dario Benedetti (Albert Einstein Institute, Potsdam, Germany), Norbert Bodendorfer (Institute for Theoretical Physics III, FAU Erlangen Nürnberg, Germany), Mariam Bouhmadi López (CENTRA, Centro Multidisciplinar de Astrofĺsica, Lisbon), Timothy Budd (Institute for Theoretical Physics, Utrecht University, The Netherlands), Miguel Campiglia (Institute for Gravitation and the Cosmos, Penn State University, USA), Gianluca Delfino (School of Mathematical Sciences, University of Nottingham, UK), Maite Dupuis (Institute for Theoretical Physics III, FAU Erlangen Nürnberg, Germany), Michał Dziendzikowski (Institute of Theoretical Physics, Warsaw University, Poland), Muxin Han (Centre de Physique Théorique de Luminy, Marseille, France), Philipp Höhn (Institute for Theoretical Physics, Utrecht University, The

PREFACE: Workshop Photograph and Program

NASA Astrophysics Data System (ADS)

2011-07-01

: Bonnie Fleming (Yale U.))18:30 Supernovae neutrino detection (20') Ines Gil-Botella (CIEMAT)18:50 Neutrino cross-section in Liquid Argon in the GeV range (15') Flavio Cavanna (U. of L'Aquila)19:05 Analysis of the ArgoNeuT neutrino data (15') Carl Bromberg (Michigan State U.)19:20 Neutrino event reconstruction (15') Gary Barker (U. of Warwick) Tuesday 30 March 2010Ways to improve the Liquid Argon Charge Imaging technology I (Chair: Christos Touramanis (U. of Liverpool))09:00 Liquid Argon LEM TPC (30') Filippo Resnati (ETH Zurich)09:30 Micromegas for charge readout of double phase liquid Argon large TPCs (20') Alain Delbart (Saclay)09:50 Development of Thick-GEMs for GEM-TPC Tracker (20') Fuminori Sakuma (RIKEN)10:10 Optical readout of the ionization (20') Neil Spooner (U. of Sheffield)10:30 Scintillation light readout (20') Kostas Mavrokoridis (U. of Liverpool)10:50-11:10 Coffee break Ways to improve the Liquid Argon Charge Imaging technology II (Chair: Alberto Marchionni (ETH Zurich))11:10 Development of cold electronics (30') Veljko Radeka (BNL)11:40 Development of a frontend ASIC and DAQ system Dario Autiero (IPN Lyon)12:00 CAEN digitizers (20') Carlo Tintori (CAEN)12:20 Recent results from Liquid Argon R&D activity (20') Masashi Tanaka (KEK)12:40 Results from the materials test stand and status of LAPD (20') Brian Rebel (FNAL)13:00 Purging and purification: 6 m3 @CERN (20') Alessandro Curioni (ETH Zurich)13:20-14:30 Lunch break14:30-20:00 Trip to J-PARC to visit T2K Beam Facility and Near Detector20:00-22:00 Workshop dinner at Okura Frontier Hotel Tsukuba Wednesday 31 March 2010Ways to improve the Liquid Argon Charge Imaging technology III (Chair: Takasumi Maruyama (KEK))09:00 ArgonTube and UV laser ionization (25') Biagio Rossi (U. of Bern)09:25 Detector magnetization (15') Andreas Badertscher (ETH Zurich)09:40 HV system (25') Sosuke Horikawa (ETH Zurich) Localization studies (Chair: Takuya Hasegawa (KEK))10:05 Okinoshima site study (20') Masakazu Yoshioka (KEK)10

PREFACE: First Mediterranean Conference on Classical and Quantum Gravity (MCCQG 2009)

NASA Astrophysics Data System (ADS)

Basilakos, Spyros; Cadoni, Mariano; Cavaglia, Marco; Christodoulakis, Theodosios; Vagenas, Elias C.

2010-04-01

Fisica, Universidade de Sao Paulo, Brasil) Antoniadis, Ignatios (CERN, Geneva, Switzerland) Arminjon, Mayeul (CNRS, Section of Theoretical Physics, France) Banados, Max (University of Oxford, UK) Basilakos, Spyros (RCAAM, Academy of Athens, Greece) Bastos, Catarina (IST, Departamento de Física, Portugal) Bertolami, Orfeu (IST, Departamento de Física, Portugal) Bevilaqua, Leandro Ibiapina (Instituto de Fisica, Universidade de Sao Paulo, Brazil) Bezerra De Mello, Eugenio (Dept. de Física, CCEN Universidade Federal da Paraíba, Brazil) Blake, Russ (Readify Pty Ltd, Australia) Bogdanos, Charalampos (LPT-Orsay, France) Burinskii, Alexander (Gravity Research Group NSI, Russian Academy of Sciences, Russia) Cadonati, Laura (University of Massachusetts, Amherst, USA) Cadoni, Mariano (Università di Cagliari, Italy) Capone, Monica (University of Turin, Italy) Cavaglià, Marco (University of Mississippi, USA) Chirco, Goffredo (SISSA-International School for Advanced Studies, Italy) Christodoulakis, Theodosios (University of Athens, Greece) Domingues Zarro, Carlos Augusto ((IST, Departamento de Física, Portugal) Durrer, Ruth (Université de Genève, Département de Physique Théorique, Switzerland) Fagnocchi, Serena (SISSA-International School for Advanced Studies, Italy) Finazzi, Stefano (SISSA-International School for Advanced Studies, Italy) Francia, Dario (University Paris 7 - APC, France) Ghosh, Subir (Indian Statistical Institute, India) Gomberoff, Andres (Universidad Catolica de Chile, Chile) Grumiller, Daniel (Institute for Theoretical Physics Vienna University of Technology, Austria) Herrera-Aguilar, Alfredo (IFM, Universidad Michoacana de San Nicolas de Hidalgo, Mexico) Hsu, Steve (University of Oregon, USA) Ichinose, Shoichi (University of Shizuoka, SFNS, Japan) Kiefer, Claus (Institute for Theoretical Physics, University of Cologne, Germany) Kokkotas, Kostas (Theoretical Astrophysics, Eberhard Karls University of Tuebingen, Germany) Kothawala, Dawood (IUCAA, Pune

PREFACE New developments in nanopore research—from fundamentals to applications New developments in nanopore research—from fundamentals to applications

NASA Astrophysics Data System (ADS)

Albrecht, Tim; Edel, Joshua B.; Winterhalter, Mathias

2010-11-01

, Di Cao and Stuart Lindsay Probing DNA with micro- and nanocapillaries and optical tweezers L J Steinbock, O Otto, D R Skarstam, S Jahn, C Chimerel, J L Gornall and U F Keyser Fabrication of nanopores with embedded annular electrodes and transverse carbon nanotube electrodes Zhijun Jiang, Mirna Mihovilovic, Jason Chan and Derek Stein Fabrication and electrical characterization of a pore-cavity-pore device D Pedone, M Langecker, A M Münzer, R Wei, R D Nagel and U Rant Use of tunable nanopore blockade rates to investigate colloidal dispersions G R Willmott, R Vogel, S S C Yu, L G Groenewegen, G S Roberts, D Kozak, W Anderson and M Trau Facilitated translocation of polypeptides through a single nanopore Robert Bikwemu, Aaron J Wolfe, Xiangjun Xing and Liviu Movileanu Mechanistic insight into gramicidin-based detection of protein-ligand interactions via sensitized photoinactivation Tatyana I Rokitskaya, Michael X Macrae, Steven Blake, Natalya S Egorova, Elena A Kotova, Jerry Yang and Yuri N Antonenko Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy Stephan Renner, Andrey Bessonov, Ulrich Gerland and Friedrich C Simmel Hydration properties of mechanosensitive channel pores define the energetics of gating A Anishkin, B Akitake, K Kamaraju, C-S Chiang and S Sukharev Dynamic translocation of ligand-complexed DNA through solid-state nanopores with optical tweezers Andy Sischka, Andre Spiering, Maryam Khaksar, Miriam Laxa, Janine König, Karl-Josef Dietz and Dario Anselmetti Force fluctuations assist nanopore unzipping of DNA V Viasnoff, N Chiaruttini, J Muzard and U Bockelmann Control and reversal of the electrophoretic force on DNA in a charged nanopore Binquan Luan and Aleksei Aksimentiev The properties of the outer membrane localized Lipid A transporter LptD Raimund Haarmann, Mohamed Ibrahim, Mara Stevanovic, Rolf Bredemeier and Enrico Schleiff Structural and dynamical properties of the porins OmpF and OmpC: insights from

Sensing at the nanoscale

NASA Astrophysics Data System (ADS)

Demming, Anna; Hierold, Christofer

2013-11-01

The merits of nanostructures in sensing may seem obvious, yet playing these attributes to their maximum advantage can be a work of genius. As fast as sensing technology is improving, expectations are growing, with demands for cheaper devices with higher sensitivities and an ever increasing range of functionalities and compatibilities. At the same time tough scientific challenges like low power operation, noise and low selectivity are keeping researchers busy. This special issue on sensing at the nanoscale with guest editor Christofer Hierold from ETH Zurich features some of the latest developments in sensing research pushing at the limits of current capabilities. Cheap and easy fabrication is a top priority. Among the most popular nanomaterials in sensing are ZnO nanowires and in this issue Dario Zappa and colleagues at Brescia University in Italy simplify an already cheap and efficient synthesis method, demonstrating ZnO nanowire fabrication directly onto silicon substrates [1]. Meanwhile Nicolae Barson and colleagues in Germany point out the advantages of flame spray pyrolysis fabrication in a topical review [2] and, maximizing on existing resources, researchers in Denmark and Taiwan report cantilever sensing using a US20 commercial DVD-ROM optical pickup unit as the readout source [3]. The sensor is designed to detect physiological concentrations of soluble urokinase plasminogen activator receptor, a protein associated with inflammation due to HIV, cancer and other infectious diseases. With their extreme properties carbon nanostructures feature prominently in the issue, including the demonstration of a versatile and flexible carbon nanotube strain sensor [4] and a graphene charge sensor with sensitivities of the order of 1.3 × 10-3 e Hz-1/2 [5]. The issue of patterning for sensing devices is also tackled by researchers in the US who demonstrate a novel approach for multicomponent pattering metal/metal oxide nanoparticles on graphene [6]. Changes in electrical

PREFACE: Fourth Meeting on Constrained Dynamics and Quantum Gravity

NASA Astrophysics Data System (ADS)

Cadoni, Mariano; Cavaglia, Marco; Nelson, Jeanette E.

2006-04-01

Cagliari, Italy) Roberto De Pietri (Università di Parma, Italy) Giuseppe De Risi (Università di Bari, Italy) Hans-Thomas Elze (Univ. Federal do Rio de Janeiro, Brasil) Alessandro Fabbri (Università di Bologna, Italy) Sergey Fadeev (VNIIMS, Moscow, Russia) Serena Fagnocchi (Università di Bologna, Italy) Sara Farese (Universidad de Valencia, Spain) Alessandra Feo (Università di Parma, Italy) Dario Francia (Università di Roma Tor Vergata, Italy) Francesco Fucito (Università di Roma Tor Vergata, Italy) Dmitri Fursaev (JINR, Dubna, Russia) Daniel Galehouse (University of Akron, Ohio, USA) Remo Garattini (Università di Bergamo, Italy) Florian Girelli (Perimeter Institute, Waterloo, Canada) Luca Griguolo (Università di Parma, Italy) Daniel Grumiller (Universität Leipzig, Germany) Shinichi Horata (Hayama Center of Advanced Research, Japan) Giorgio Immirzi (Università di Perugia, Italy) Roman Jackiw (MIT, Cambridge, USA) Matyas Karadi (DAMTP, University of Cambridge, UK) Mikhail Katanaev (Steklov Mathematical Institute, Moscow, Russia) Claus Kiefer (Universität Koln, Germany) John Klauder (University of Florida, Gainesville, USA) Pavel Klepac (Masaryk University, Brno, Czech Republic) Jen-Chi Lee (National Chiao-Tung University, Taiwan) Carlos Leiva (Universidad de Tarapacá, Arica, Chile) Stefano Liberati (SISSA/ISAS, Trieste, Italy) Jorma Louko (University of Nottingham, UK) Luca Lusanna (INFN, Sezione di Firenze, Italy) Roy Maartens (University of Portsmouth, UK) Fotini Markopoulou (Perimeter Institute, Waterloo, Canada) Annalisa Marzuoli (Università di Pavia, Italy) Evangelos Melas (QMW, University of London, UK) Maurizio Melis (Università di Cagliary, Italy) Vitaly Melnikov (VNIIMS, Moscow, Russia) Guillermo A. Mena Marugan (CSIC, Madrid, Spain) Pietro Menotti (Università di Pisa, Italy) Salvatore Mignemi (Università di Cagliari, Italy) Aleksandar Mikovic (Universidade Lusófona, Lisboa, Portugal) Leonardo Modesto (Université de la Mediterranée, Marseille