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Novel SNP improves differential survivability and mortality in non-small cell lung cancer patients

BMC Genomics 2014年第9期15卷 1-7页

作者： Mah, Tzia Liang Yap, Xin Ning Adeline Limviphuvadh, Vachiranee Li, Nanpu Sridharan, Srinath Kuralmani, Vellaisemy Feng, Mengling Liem, Natalia Adhikari, Sharmila Yong, Wei Peng Soo, Ross A Maurer-Stroh, Sebastian Eisenhaber, Frank Tong, Joo Chuan Institute for Infocomm Research Data Analytics Department 1 Fusionopolis Way #21-01 Connexis South Tower Singapore 138632 Singapore National University Health System Department of Haematology-Oncology 5 Lower Kent Ridge Road Singapore 119074 Singapore Bioinformatics Institute 30 Biopolis Street #07-01 Matrix Singapore 138671 Singapore Nanyang Technological University (NTU) School of Biological Sciences (SBS) 60 Nanyang Drive 637551 Singapore Nanyang Technological University (NTU) School of Computer Engineering (SCE) 50 Nanyang Drive 637553 Singapore National University of Singapore (NUS) Department of Biological Sciences (DBS) 8 Medical Drive 4 117597 Singapore National University of Singapore Department of Biochemistry Yong Loo Lin School of Medicine Singapore 117597 Singapore Institute of High Performance Computing 1 Fusionopolis Way #16-16 Connexis 138632 Singapore National University of Singapore Cancer Science Institute of Singapore Singapore

Background: Non-small cell lung cancer (NSCLC) is a major cause of cancer-related death worldwide due to poor patient prognosis and clinical outcome. Here, we studied the genetic variations underlying NSCLC pathogenesis based on their association to patient outcome after gemcitabine therapy. Results: Bioinformatics analysis was used to investigate possible effects of POLA2 G583R (POLA2+1747 GG/GA, dbSNP ID: rs487989) in terms of protein function. Using biostatistics, POLA2+1747 GG/GA (rs487989, POLA2 G583R) was identified as strongly associated with mortality rate and survival time among NSCLC patients. It was also shown that POLA2+1747 GG/GA is functionally significant for protein localization via green fluorescent protein (GFP)-tagging and confocal laser scanning microscopy analysis. The single nucleotide polymorphism (SNP) causes DNA polymerase alpha subunit B to localize in the cytoplasm instead of the nucleus. This inhibits DNA replication in cancer cells and confers a protective effect in individuals with this SNP. Conclusions: The results suggest that POLA2+1747 GG/GA may be used as a prognostic biomarker of patient outcome in NSCLC pathogenesis. © 2014 Mah et al.;licensee BioMed Central Ltd.

关键词： Biomarker Genetic variant Mortality Non-small cell lung cancer Survival Outcome

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ICTNET at Microblog Track in TREC 2013 22

ICTNET at Microblog Track in TREC 2013

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22nd Text REtrieval Conference, TREC 2013

作者： Gao, Jinhua Cui, Guoxin Liu, Shenghua Liu, Yue Cheng, Xueqi Center of Web Data Science and Engineering Institute of Computing Technology Chinese Academy of Sciences Beijing100190 China University of Chinese Academy of Sciences Beijing100190 China

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Grids, virtualization, and clouds at Fermilab

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Journal of Physics: Conference Series 2014年第3期513卷

作者： S Timm K Chadwick G Garzoglio S Noh Scientific Computing Division Fermi National Accelerator Laboratory USA To whom any correspondence should be addressed Global Science experimental Data hub Center Korea Institute of Science and Technology Information South Korea

Fermilab supports a scientific program that includes experiments and scientists located across the globe. To better serve this community, in 2004, the (then) computing Division undertook the strategy of placing all of the High Throughput computing (HTC) resources in a Campus Grid known as FermiGrid, supported by common shared services. In 2007, the FermiGrid Services group deployed a service infrastructure that utilized Xen virtualization, LVS network routing and MySQL circular replication to deliver highly available services that offered significant performance, reliability and serviceability improvements. This deployment was further enhanced through the deployment of a distributed redundant network core architecture and the physical distribution of the systems that host the virtual machines across multiple buildings on the Fermilab Campus. In 2010, building on the experience pioneered by FermiGrid in delivering production services in a virtual infrastructure, the computing Sector commissioned the FermiCloud, General Physics computing Facility and Virtual Services projects to serve as platforms for support of scientific computing (FermiCloud 6 GPCF) and core computing (Virtual Services). This work will present the evolution of the Fermilab Campus Grid, Virtualization and Cloud computing infrastructure together with plans for the future.

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Big data analytics as a service: Exploring reuse opportunities

Big data analytics as a service: Exploring reuse opportuniti...

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IEEE International Conference on Information Reuse and Integration (IRI)

作者： Ling Liu Distributed Data Intensive Systems Lab School of Computer Science College of Computing Georgia Institute of Technology USA

Summary form only given. As data scientists, we live in interesting times. data has been the No. 1 fast growing phenomenon on the Internet for the last decade. Big data analytics have the potential to reveal deep insights hidden by big data that exceeds the processing capacity of existing systems, such as peer influence among customers, revealed by analyzing shoppers' transactions, social and geographical data. In the past 40 years, data was primarily used to record and report business activities and scientific events, and in the next 40 years data will be used also to derive new insights, to influence business decisions and to accelerate scientific discovery. The key challenge is to provide the right platforms and tools to make reasoning of big data easy and simple. In this keynote talk, I will explore reuse opportunities and challenges from multiple dimensions towards delivering big data analytics as a service. I will illustrate by example the importance and challenges of utilizing programmable algorithm abstractions for many seemingly domain-dependent data analytics tasks. Another reuse opportunity is to exploit unconventional data structures and big data processing constructs to simplify and speed up the big data processing.

关键词： Internet data analysis data structures

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Design of a high-performance full-system instrumentation

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Dongbei Daxue Xuebao/Journal of Northeastern University 2014年 35卷 129-134页

作者： Min, Qing-Hao Zhang, Zheng Wang, Hao-Jun Zhang, Wei-Hua Software School Fudan University Shanghai201203 China Shanghai Key Laboratory of Data Science Fudan University Shanghai201203 China Parallel Processing Institute Fudan University Shanghai201203 China State Key Laboratory of Mathematic Engineering and Advanced Computing PLA Information Engineering University Zhengzhou450001 China

Instrumentation is an important mechanism to collect run-time information of applications for further analysis like bottleneck analysis, hotspot analysis and even bug detection and revision. Currently there are lots of analyzers using instrumentation to collect their source data. However, most of these tools lack of full-system support and thus become inadequate for analyzing multi-core programs as they cannot provide full-system information like scheduling, system calls and inter-process communication, etc. Meanwhile, full-system instrumentation needs to collect OS and hardware information, resulting to performance degradation. In this paper, a high-performance full-system instrumentation method was designed for collecting full-system information as well as application information. The proposed method was implemented inside the QEMU full-system emulator, and 40 MIPS performance on average was achieved after optimization, which was appropriated for normal program analysis. ©, 2014, Northeastern University. All right reserved.

关键词： Full-system High-performance Instrumentation Multi-core

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Book Review: Crime Modeling and Mapping using Geospatial Technologies , Leitner, M. (Ed.). Springer Verlag, 2013, 446 pages, £ 117.00 (Hard Cover) ISBN 9789400749952, Springer Dordrecht, Heidelberg, New York, London

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Applied Spatial Analysis and Policy 2013年第4期6卷 333-336页

作者： Gary Higgs GIS Research Centre and Wales Institute of Social and Economic Research Data and Methods Faculty of Computing Engineering and Science University of South Wales Pontypridd UK

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First-principles study of perpendicular magnetic anisotropy in CoFe/MgO and CoFe/Mg3B2O6 interfaces

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Physical Review B 2013年第17期87卷 174403-174403页

作者： K. H. Khoo G. Wu M. H. Jhon M. Tran F. Ernult K. Eason H. J. Choi C. K. Gan Institute of High Performance Computing Agency for Science Technology and Research 1 Fusionopolis Way #16-16 Connexis Singapore 138632 Data Storage Institute Agency for Science Technology and Research DSI Building 5 Engineering Drive 1 Singapore 117608 Department of Physics and IPAP Yonsei University Seoul 120-749 Korea

The CoFeB/MgO interface is important not only because of its ability to act as a good spin filter, but also because it exhibits significant magnetic interface anisotropy. However, there is experimental evidence that the mineral kotoite (Mg3B2O6) forms at this interface, possibly as a result of B diffusion into the oxide. Recent calculations have demonstrated that kotoite is a surprisingly good spin filter material, despite the lack of cubic symmetry. It is not a priori clear how the perpendicular anisotropy is affected if kotoite forms at the interface. Hereby, we have performed first-principles density functional calculations to investigate the magnetic anisotropy of CoFe/kotoite interfaces. We find that the Co/Fe atoms bind strongly to O atoms of kotoite, and the CoFe/kotoite interfaces exhibit strong perpendicular magnetic anisotropy (PMA) comparable to that of CoFe/MgO interfaces. Analysis of the electronic structure shows that CoFe states having dxz and dyz character are strongly affected by the magnetization direction and play an important role in determining the magnetic anisotropy of both CoFe/kotoite and CoFe/MgO interfaces. Our observations are consistent with previous experimental observations of PMA. We demonstrate that the interface properties are only weakly affected by the formation of kotoite compared to MgO.

关键词： MAGNETIC anisotropy INTERFACES (Physical sciences) ELECTRONIC structure OXIDE minerals MAGNETIZATION

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Searching for Dark Matter Annihilation from Milky Way Dwarf Spheroidal Galaxies with Six Years of Fermi Large Area Telescope data

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Physical Review Letters 2015年第23期115卷 231301-231301页

作者： M. Ackermann A. Albert B. Anderson W. B. Atwood L. Baldini G. Barbiellini D. Bastieri K. Bechtol R. Bellazzini E. Bissaldi R. D. Blandford E. D. Bloom R. Bonino E. Bottacini T. J. Brandt J. Bregeon P. Bruel R. Buehler G. A. Caliandro R. A. Cameron R. Caputo M. Caragiulo P. A. Caraveo C. Cecchi E. Charles A. Chekhtman J. Chiang G. Chiaro S. Ciprini R. Claus J. Cohen-Tanugi J. Conrad A. Cuoco S. Cutini F. D’Ammando A. de Angelis F. de Palma R. Desiante S. W. Digel L. Di Venere P. S. Drell A. Drlica-Wagner R. Essig C. Favuzzi S. J. Fegan E. C. Ferrara W. B. Focke A. Franckowiak Y. Fukazawa S. Funk P. Fusco F. Gargano D. Gasparrini N. Giglietto F. Giordano M. Giroletti T. Glanzman G. Godfrey G. A. Gomez-Vargas I. A. Grenier S. Guiriec M. Gustafsson E. Hays J. W. Hewitt D. Horan T. Jogler G. Jóhannesson M. Kuss S. Larsson L. Latronico J. Li L. Li M. Llena Garde F. Longo F. Loparco P. Lubrano D. Malyshev M. Mayer M. N. Mazziotta J. E. McEnery M. Meyer P. F. Michelson T. Mizuno A. A. Moiseev M. E. Monzani A. Morselli S. Murgia E. Nuss T. Ohsugi M. Orienti E. Orlando J. F. Ormes D. Paneque J. S. Perkins M. Pesce-Rollins F. Piron G. Pivato T. A. Porter S. Rainò R. Rando M. Razzano A. Reimer O. Reimer S. Ritz M. Sánchez-Conde A. Schulz N. Sehgal C. Sgrò E. J. Siskind F. Spada G. Spandre P. Spinelli L. Strigari H. Tajima H. Takahashi J. B. Thayer L. Tibaldo D. F. Torres E. Troja G. Vianello M. Werner B. L. Winer K. S. Wood M. Wood G. Zaharijas S. Zimmer Deutsches Elektronen Synchrotron DESY D-15738 Zeuthen Germany W. W. Hansen Experimental Physics Laboratory Kavli Institute for Particle Astrophysics and Cosmology Department of Physics and SLAC National Accelerator Laboratory Stanford University Stanford California 94305 USA Department of Physics Stockholm University AlbaNova SE-106 91 Stockholm Sweden The Oskar Klein Centre for Cosmoparticle Physics AlbaNova SE-106 91 Stockholm Sweden Santa Cruz Institute for Particle Physics Department of Physics and Department of Astronomy and Astrophysics University of California at Santa Cruz Santa Cruz California 95064 USA Università di Pisa and Istituto Nazionale di Fisica Nucleare Sezione di Pisa I-56127 Pisa Italy Istituto Nazionale di Fisica Nucleare Sezione di Trieste I-34127 Trieste Italy Dipartimento di Fisica Università di Trieste I-34127 Trieste Italy Istituto Nazionale di Fisica Nucleare Sezione di Padova I-35131 Padova Italy Dipartimento di Fisica e Astronomia “G. Galilei” Università di Padova I-35131 Padova Italy Dept. of Physics and Wisconsin IceCube Particle Astrophysics Center University of Wisconsin Madison Wisconsin 53706 USA Istituto Nazionale di Fisica Nucleare Sezione di Pisa I-56127 Pisa Italy Istituto Nazionale di Fisica Nucleare Sezione di Bari I-70126 Bari Italy Istituto Nazionale di Fisica Nucleare Sezione di Torino I-10125 Torino Italy Dipartimento di Fisica Generale “Amadeo Avogadro” Università degli Studi di Torino I-10125 Torino Italy NASA Goddard Space Flight Center Greenbelt Maryland 20771 USA Laboratoire Univers et Particules de Montpellier Université Montpellier CNRS/IN2P3 Montpellier France Laboratoire Leprince-Ringuet École polytechnique CNRS/IN2P3 Palaiseau France Consorzio Interuniversitario per la Fisica Spaziale (CIFS) I-10133 Torino Italy INAF-Istituto di Astrofisica Spaziale e Fisica Cosmica I-20133 Milano Italy Istituto Nazionale di Fisica Nucleare Sezione di Perugia I-06123 Perugia Italy Dipartimento di Fisica Uni

The dwarf spheroidal satellite galaxies (dSphs) of the Milky Way are some of the most dark matter (DM) dominated objects known. We report on γ-ray observations of Milky Way dSphs based on six years of Fermi Large Area Telescope data processed with the new Pass8 event-level analysis. None of the dSphs are significantly detected in γ rays, and we present upper limits on the DM annihilation cross section from a combined analysis of 15 dSphs. These constraints are among the strongest and most robust to date and lie below the canonical thermal relic cross section for DM of mass ≲100 GeV annihilating via quark and τ-lepton channels.

关键词： Gamma ray astronomy Particle dark matter Normal galaxies

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Updated search for spectral lines from Galactic dark matter interactions with pass 8 data from the Fermi Large Area Telescope

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Physical Review D 2015年第12期91卷 122002-122002页

作者： M. Ackermann M. Ajello A. Albert B. Anderson W. B. Atwood L. Baldini G. Barbiellini D. Bastieri R. Bellazzini E. Bissaldi R. D. Blandford E. D. Bloom R. Bonino E. Bottacini T. J. Brandt J. Bregeon P. Bruel R. Buehler S. Buson G. A. Caliandro R. A. Cameron R. Caputo M. Caragiulo P. A. Caraveo C. Cecchi E. Charles A. Chekhtman J. Chiang G. Chiaro S. Ciprini R. Claus J. Cohen-Tanugi J. Conrad A. Cuoco S. Cutini F. D’Ammando A. de Angelis F. de Palma R. Desiante S. W. Digel L. Di Venere P. S. Drell A. Drlica-Wagner C. Favuzzi S. J. Fegan A. Franckowiak Y. Fukazawa S. Funk P. Fusco F. Gargano D. Gasparrini N. Giglietto F. Giordano M. Giroletti G. Godfrey G. A. Gomez-Vargas I. A. Grenier J. E. Grove S. Guiriec M. Gustafsson J. W. Hewitt A. B. Hill D. Horan G. Jóhannesson R. P. Johnson M. Kuss S. Larsson L. Latronico J. Li L. Li F. Longo F. Loparco M. N. Lovellette P. Lubrano D. Malyshev M. Mayer M. N. Mazziotta J. E. McEnery P. F. Michelson T. Mizuno A. A. Moiseev M. E. Monzani A. Morselli S. Murgia E. Nuss T. Ohsugi M. Orienti E. Orlando J. F. Ormes D. Paneque M. Pesce-Rollins F. Piron G. Pivato S. Rainò R. Rando M. Razzano A. Reimer T. Reposeur S. Ritz M. Sánchez-Conde A. Schulz C. Sgrò E. J. Siskind F. Spada G. Spandre P. Spinelli H. Tajima H. Takahashi J. B. Thayer L. Tibaldo D. F. Torres G. Tosti E. Troja G. Vianello M. Werner B. L. Winer K. S. Wood M. Wood G. Zaharijas S. Zimmer Deutsches Elektronen Synchrotron DESY D-15738 Zeuthen Germany Department of Physics and Astronomy Kinard Lab of Physics Clemson University Clemson South Carolina 29634-0978 USA W.W. Hansen Experimental Physics Laboratory Kavli Institute for Particle Astrophysics and Cosmology Department of Physics and SLAC National Accelerator Laboratory Stanford University Stanford California 94305 USA Department of Physics Stockholm University AlbaNova SE-106 91 Stockholm Sweden The Oskar Klein Centre for Cosmoparticle Physics AlbaNova SE-106 91 Stockholm Sweden Department of Physics and Department of Astronomy and Astrophysics Santa Cruz Institute for Particle Physics University of California at Santa Cruz Santa Cruz California 95064 USA Università di Pisa and Istituto Nazionale di Fisica Nucleare Sezione di Pisa I-56127 Pisa Italy Istituto Nazionale di Fisica Nucleare Sezione di Trieste I-34127 Trieste Italy Dipartimento di Fisica Università di Trieste I-34127 Trieste Italy Istituto Nazionale di Fisica Nucleare Sezione di Padova I-35131 Padova Italy Dipartimento di Fisica e Astronomia “G. Galilei ” Università di Padova I-35131 Padova Italy Istituto Nazionale di Fisica Nucleare Sezione di Pisa I-56127 Pisa Italy Istituto Nazionale di Fisica Nucleare Sezione di Bari 70126 Bari Italy Istituto Nazionale di Fisica Nucleare Sezione di Torino I-10125 Torino Italy Dipartimento di Fisica Generale “Amadeo Avogadro ” Università degli Studi di Torino I-10125 Torino Italy NASA Goddard Space Flight Center Greenbelt Maryland 20771 USA Laboratoire Univers et Particules de Montpellier Université Montpellier CNRS/IN2P3 Montpellier France Laboratoire Leprince-Ringuet École polytechnique CNRS/IN2P3 Route de Saclay F91128 Palaiseau France Consorzio Interuniversitario per la Fisica Spaziale (CIFS) I-10133 Torino Italy INAF-Istituto di Astrofisica Spaziale e Fisica Cosmica I-20133 Milano Italy Istituto Nazionale di Fisica Nucleare Sezione di Perugia I-06123 Perugia Italy Dipartime

Dark matter in the Milky Way may annihilate directly into γ rays, producing a monoenergetic spectral line. Therefore, detecting such a signature would be strong evidence for dark matter annihilation or decay. We search for spectral lines in the Fermi Large Area Telescope observations of the Milky Way halo in the energy range 200 MeV–500 GeV using analysis methods from our most recent line searches. The main improvements relative to previous works are our use of 5.8 years of data reprocessed with the Pass 8 event-level analysis and the additional data resulting from the modified observing strategy designed to increase exposure of the Galactic center region. We search in five sky regions selected to optimize sensitivity to different theoretically motivated dark matter scenarios and find no significant detections. In addition to presenting the results from our search for lines, we also investigate the previously reported tentative detection of a line at 133 GeV using the new Pass 8 data.

关键词： SPECTRAL lines DARK matter (Astronomy) ATOMIC spectra FERMI energy ELECTRONIC structure MILKY Way

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A Generic Construction of Proxy Signatures from Certificateless Signatures

A Generic Construction of Proxy Signatures from Certificatel...

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International Conference on Advanced Information Networking and Applications (AINA)

作者： Lei Zhang Qianhong Wu Bo Qin Josep Domingo-Ferrer Peng Zeng Jianwei Liu Ruiying Du Shanghai Key Laboratory of Trustworthy Computing Software Engineering Institute East China Normal University Shanghai China UNESCO Chair in Data Privacy Department of Computer Engineering and Mathematics Universitat Rovira i Virgili Tarragona Spain Key Laboratory of Aerospace Information Security and Trusted Computing Ministry of Education School of Computer Wuhan University China Department of Maths School of Science Xi'an University of Technology China School of Electronic and Information Engineering Beijing University of Aeronautics and Astronautics China

The primitive of proxy signatures allows the original signer to delegate proxy signers to sign on messages on behalf of the original signer. It has found numerous applications in distributed computing scenarios where delegation of signing rights is common. Certificate less public key cryptography eliminates the complicated certificates in traditional public key cryptosystems without suffering from the key escrow problem in identity-based public key cryptography. In this paper, we reveal the relationship between the two important primitives of proxy signatures and certificate less signatures and present a generic conversion from the latter to the former. Following the generic transformation, we propose an efficient proxy signature scheme with a recent certificate less signature scheme.

关键词： Artificial intelligence Bismuth Games Public key cryptography Educational institutions

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