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BioN∅T: A searchable database of biomedical negated sentences

BMC Bioinformatics 2011年第1期12卷 1-7页

作者： Agarwal, Shashank Yu, Hong Kohane, Issac Medical Informatics College of Engineering and Applied Sciences University of Wisconsin-Milwaukee 3200 N. Cramer St. Milwaukee WI 53201-0784 United States Department of Computer Science and Electrical Engineering College of Engineering and Applied Sciences University of Wisconsin-Milwaukee 3200 N. Cramer St. Milwaukee WI 53201-0784 United States Department of Health Sciences College of Health Science University of Wisconsin-Milwaukee 2400 E. Hartford Ave. Milwaukee WI 53211 United States Children's Hospital Informatics Program Children's Hospital 300 Longwood Ave. Enders-6 Boston MA 02115 United States

Background: Negated biomedical events are often ignored by text-mining applications;however, such events carry scientific significance. We report on the development of BioN∅T, a database of negated sentences that can be used to extract such negated ***: Currently BioN∅T incorporates ≈32 million negated sentences, extracted from over 336 million biomedical sentences from three resources: ≈2 million full-text biomedical articles in Elsevier and the PubMed Central, as well as ≈20 million abstracts in PubMed. We evaluated BioN∅T on three important genetic disorders: autism, Alzheimer's disease and Parkinson's disease, and found that BioN∅T is able to capture negated events that may be ignored by ***: The BioN∅T database can be a useful resource for biomedical researchers. BioN∅T is freely available at http://***/. In future work, we will develop semantic web related technologies to enrich BioN∅T. © 2011 Agarwal et al;licensee BioMed Central Ltd.

关键词： Database systems

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Poster abstracts

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Sleep and Biological Rhythms 2016年第1期5卷 A1-A189页

作者： J. Ferrie M. Shipley F. Cappuccio E. Brunner M. Miller M. Kumari M. Marmot A. Coenen J. L. Castillo F. Araya G. Bustamante L. Montecino C. Torres S. Oporto J. Gronli E. Fiske R. Murison B. Bjorvatn E. Sorensen R. Ursin C. M. Portas S. Rajaraman A. Gribok N. Wesensten T. Balkin J. Reifman N. Dursunoglu S. Ozkurt S. Baser O. Delen S. Sarikaya P. Sadler P. Mitchell D. Françon M. Decobert B. Herve A. Richard G. Griebel P. Avenet B. Scatton G. L. Fur D. Eckert A. Jordan A. Wellman S. Smith A. Malhotra D. White D. Bruck I. Thomas A. Kritikos W. Oertel K. Stiasny-Kolster D. Garcia-Borreguero W. Poewe B. Hoegl R. Kohnen E. Schollmayer J. Keffel C. Trenkwalder A. Valle S. Roizenblatt F. Fregni P. Boggio S. Tufik K. Ward L. Robertson L. Palmer P. Eastwood D. Hillman J. Lee S. Mukherjee V. de Padova G. Barbato G. Ficca I. Zilli P. Salzarulo M. Veldi T. Hion V. Vasar M. Kull L. Nowak J. Davis Y. Latzer O. Tzischinsky S. Crowley M. Carskadon M. Anca-Herschkovitsch D. Frey J. Ortega C. Wiseman C. Farley K. Wright A. Campbell A. Neill K. Spiegel R. Leproult E. Tasali N. Scherberg E. van Cauter A. T. Noradina N. A. Karim I. Norlinah A. A. Raymond R. Sahathevan B. Hamidon E. Werth R. Poryazova R. Khatami C. Bassetti R. G. Beran L. Ainley G. Holand J. Duncan H. Kinney B. Davis B. Hood S. Frey C. Schmidt M. Hofstetter P. Peigneux C. Cajochen W.-P. Hu J.-D. Li C. Zhang L. Boehmer J. Siegel Q.-Y. Zhou Y. Sagawa H. Kondo T. Takemura H. Kanayama Y. Kaneko M. Sato T. Kanbayashi Y. Hishikawa T. Shimizu A. Viola L. James L. Schlangen D.-J. Dijk R. Andretic Y.-C. Kim K.-A. Han F. Jones R. Greenspan L. Sanford L. Yang X. Tang K. Dieter E. Uta H. Sven M. Richard N. Oyane S. Pallesen F. Holsten Y. Inoue M. Fujita N. Emura K. Kuroda N. Uchimura A. Johnston J. Astbury G. Kennedy K. Hoedlmoser M. Schabus T. Pecherstorfer S. Moser G. Gruber P. Anderer W. Klimesch N. Naidoo M. Ferber A. Pack D. Neu O. Mairesse G. Hoffmann A. Dris L. Lambrecht P. Linkowski P. Verbanck O. Le Bon N. Matsuura M. Yamao N. Adachi R. Aritomi Y. Komada H. Tanaka S. Shirak University College London London UK University College London London USA Warwick Medical School London UK Warwick Medical School Coventry USA Radboud University Nijmegen Nijmegen Netherlands Department of Neurology University of Chile Santiago Chile Neurology Service Hospital del Salvador Santiago Chile Family Health Center Juan Pablo II Santiago Chile Department of Biomedicine Section on Physiology Univeristy of Bergen Bergen Norway Department of Public Health and Primary Health Care Univeristy of Bergen Bergen Norway Department of Public Health and Primary Health Care University of Bergen Bergen Norway Norwegian Competence Center for Sleep Disorders Haukeland University Hospital Bergen Norway Department of Child and Adolescent Psychiatry Haukeland University Hospital Univeristy of Bergen Bergen Norway Department of Biomedicine University of Bergen Bergen Norway US Army Medical Research and Materiel Command Fort Detrick Frederick USA Walter Reed Army Institute of Research Silver Spring USA Department of Behavioral Biology Walter Reed Army Institute of Research Silver Spring USA Faculty Department of Pulmonology Pamukkale University Medical Denizli Turkey University of Ballarat Ballarat Australia Sanofi-Aventis Recherche et Developpement Paris France Brigham and Women’s Hospital Harvard Medical School Boston USA The University of Queensland Adelaide Australia School of Psychology University of Queensland Brisbane Australia The University of Queensland Brisbane Australia Victoria University Melbourne Australia Department of Psychology Victoria University Melbourne Australia School of Psychology Victoria University Melbourne Australia Philips-Universität Marburg Germany Philips-Universitaet-Marburg Marburg Germany Instituto de Investigaciones del Sueno Madrid Spain Universitätsklinik für Neurologie Innsbruck Austria Universitaetsklinik fuer Neurologie Innsbruck Austria IMEREM GmbH Nuernberg Germany Schwarz Pharma AG Monheim Germany

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Summation convolution filtered back projection and algebraic reconstruction technique for ring array ultrasound tomography based on time of flight

Summation convolution filtered back projection and algebraic...

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International Conference on Instrumentation Control and Automation (ICA)

作者： K. Ain D. Kurniadi A. Trisnobudi O. Santoso Physics Department Airlangga University Surabaya Indonesia Engineering Physics Program Institut Teknologi Bandung Bandung Indonesia Informatics Program Institut Teknologi Bandung Bandung Indonesia

Purpose of the study is to apply SCFBP and ART methods on a ring array ultrasound tomography system based on time of flight. The study was conducted with numerical and experimental object by 16 positions in circular phantom. The data set of ring array was rearranged and interpolated into parallel scheme to reconstructed by SCFBP and ART methods. The result indicated that rearrangement and interpolation is feasible to use SCFBP methods, improve speed and reconstructed image quality on ART methods.

关键词： Biomedical imaging Subspace constraints Transmitters Generators Image reconstruction

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Handling failures of static sensor nodes in wireless sensor network by use of mobile sensors

Handling failures of static sensor nodes in wireless sensor ...

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25th IEEE International Conference on Advanced Information Networking and Applications Workshops, WAINA 2011

作者： Pignaton De Freitas, Edison Heimfarth, Tales Netto, Ivayr Farah Pereira, Carlos Eduardo Ferreira, Armando Morado Wagner, Flávio Rech Larsson, Tony IDE Halmstad University Halmstad Sweden Institute of Informatics Federal University of Rio Grande Do Sul Porto Alegre Brazil Computer Science Department Federal University of Lavras Lavras Brazil Electrical Engineering Department Federal University of Rio Grande Do Sul Porto Alegre Brazil Defense Engineering Graduate Program Military Institute of Engineering Rio de Janeiro Brazil

ISBN: (纸本)9780769543383

Node failures in Wireless Sensor Networks composed by static sensor nodes are common due to the nature of the sensor devices and the usually harsh environments in which they are deployed. Node failures can diminish the performance of the network as a whole, thus affecting its functionality in delivering the desired services. For instance, significant regions can become uncovered due to failure of several nearby nodes. This paper reports a study about the use of mobile sensor nodes acting in cooperation with static ones in order to fill gaps created by faulty static nodes. The proposed fault handling mechanism presents alternative policies with pros and cons, depending on the user priorities imposed to the system and the occurrence of failures. A discussion about this topic is presented based on results obtained by simulation of the proposed mechanisms. © 2011 IEEE.

关键词： Sensor nodes

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Generalized Enhanced Multivariance Product Representation for Data Partitioning: Constancy Level

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AIP Conference Proceedings 2011年第1期1389卷 1152-1155页

作者： M. Alper Tunga Metin Demiralp aBahçeşehir University Faculty of Engineering Software Engineering Department Beşiktaş 34349 İstanbul Turkey bİstanbul Technical University Informatics Institute Computational Science and Engineering Program Maslak 34469 İstanbul Turkey

Enhanced Multivariance Product Representation (EMPR) method is used to represent multivariate functions in terms of less‐variate structures. The EMPR method extends the HDMR expansion by inserting some additional support functions to increase the quality of the approximants obtained for dominantly or purely multiplicative analytical structures. This work aims to develop the generalized form of the EMPR method to be used in multivariate data partitioning approaches. For this purpose, the Generalized HDMR philosophy is taken into consideration to construct the details of the Generalized EMPR at constancy level as the introductory steps and encouraging results are obtained in data partitioning problems by using our new method. In addition, to examine this performance, a number of numerical implementations with concluding remarks are given at the end of this paper.

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Text and file encryption application for blackberry using cipher feedback 8-bit mode

Text and file encryption application for blackberry using ci...

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International Conference on Electrical engineering and informatics, ICEEI

作者： Matthew Wangsadiredja Rinaldi Munir Informatics Engineering Study Program Bandung Institute of Technology Bandung Indonesia Institut Teknologi Bandung Bandung Jawa Barat ID

BlackBerry is not just an ordinary smartphone which rich in its multimedia features. BlackBerry also has very reliable internet services, include BlackBerry Messenger, e-mail, other instant messaging, and other internet service that Blackberry Internet Service (BIS) covers. However, there's an open question that all services that go through BIS is safe or not; considering the data includes text and files which is sent through BIS have to pass through the main server which is located in Canada. Therefor in this paper we chose to make software that can encrypt and decrypt text and even files, which will be sent through BlackBerry's internet or just to be stored in the BlackBerry device. In this paper, we use cipher block encryption algorithm with Cipher Feedback (CFB) 8-bit mode. This mode is chosen because it suits with the data inside BlackBerry device which is 8-bit aligned. The encryption algorithm uses cipher block encryption with 64-bit block size. We designed the algorithm based on Feistel network combined with some encryption/decryption algorithm. Then the cipher block encryption algorithm is implemented in software based on Java for BlackBerry. In this software development, we use the IDE Eclipse Ganymede with certain plugins. The expected result is software for BlackBerry capable to encrypt and decrypt some texts, either directly typed or saved as files on the BlackBerry device. This software also handles specific file types, such as picture and audio by preserving their file header, and also handles text encryption by transforming the ciphertext data to hex digits. After conducting some experiments, we conclude that the software has good compatibility with many kinds of BlackBerry devices and has good security level.

关键词： Encryption Software Algorithm design and analysis Software algorithms Servers Web and internet services

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Integration of Multilayers in Er-Doped Porous Silicon Structures and Advances in 1.5 μm Optoelectronic Devices

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MRS Online Proceedings Library 2011年第1期536卷 135-140页

作者： H. A. Lopez S. Chan L. Tsybeskov H. Koyama V. P. Bondarenko P. M. Fauchet Materials Science Program University of Rochester Rochester USA Department of Electrical and Computer Engineering University of Rochester Rochester USA Belarusian State University of Informatics and Radioelectronics Minsk Belarus

Infrared photoluminescence (PL) and electroluminescence (EL) from erbium-doped porous silicon (PSi) structures are studied. The PL and EL from the Er-doped PSi structures and the absence of silicon band edge recombination, point defect, and dislocation luminescence bands suggest that the Er-complex centers are the most efficient recombination sites. PSi multilayers with very high reflectivity (R ≥ 90%) in the 1.5 gim range have been incorporated in the structures resulting in a PL enhancement of over 100%. Stable and intense EL is obtained from the Er-doped structures. The EL spectrum is similar to that of the PL, but shifted towards higher energy. The unexpected shift in emission opens up the possibility for erbium related luminescence to encompass a larger part of the optimal wavelength window for fiber optic communications.

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ESICM LIVES 2016: part three

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Intensive Care Medicine Experimental 2016年第1期4卷 405-607页

作者： Velasquez, T. Mackey, G. Lusk, J. Kyle, U. G. Fontenot, T. Marshall, P. Shekerdemian, L. S. Coss-Bu, J. A. Nishigaki, A. Yatabe, T. Tamura, T. Yamashita, K. Yokoyama, M. Ruiz-Rodriguez, J. C. Encina, B. Belmonte, R. Troncoso, I. Tormos, P. Riveiro, M. Baena, J. Sanchez, A. Bañeras, J. Cordón, J. Duran, N. Ruiz, A. Caballero, J. Nuvials, X. Riera, J. Serra, J. Rutten, A. M. F. van Ieperen, S. N. M. Der Kinderen, E. P. H. M. Van Logten, T. Kovacikova, L. Skrak, P. Zahorec, M. Akcan-Arikan, A. Silva, J. C. Goldsworthy, M. Wood, D. Harrison, D. Parslow, R. Davis, P. Pappachan, J. Goodwin, S. Ramnarayan, P. Chernyshuk, S. Yemets, H. Zhovnir, V. Pulitano’, S. M. De Rosa, S. Mancino, A. Villa, G. Tosi, F. Franchi, P. Conti, G. Patel, B. Khine, H. Shah, A. Sung, D. Singer, L. Haghbin, S. Inaloo, S. Serati, Z. Idei, M. Nomura, T. Yamamoto, N. Sakai, Y. Yoshida, T. Matsuda, Y. Yamaguchi, Y. Takaki, S. Yamaguchi, O. Goto, T. Longani, N. Medar, S. Abdel-Aal, I. R. El Adawy, A. S. Mohammed, H. M. E. H. Mohamed, A. N. Parry, S. M. Knight, L. D. Denehy, L. De Morton, N. Baldwin, C. E. Sani, D. Kayambu, G. da Silva, V. Z. M. Phongpagdi, P. Puthucheary, Z. A. Granger, C. L. Rydingsward, J. E. Horkan, C. M. Christopher, K. B. McWilliams, D. Jones, C. Reeves, E. Atkins, G. Snelson, C. Aitken, L. M. Rattray, J. Kenardy, J. Hull, A. M. Ullman, A. Le Brocque, R. Mitchell, M. Davis, C. Macfarlane, B. Azevedo, J. C. Rocha, L. L. De Freitas, F. F. M. Cavalheiro, A. M. Lucinio, N. M. Lobato, M. S. Ebeling, G. Kraegpoeth, A. Laerkner, E. De Brito-Ashurst, I. White, C. Gregory, S. Forni, L. G. Flowers, E. Curtis, A. Wood, C. A. Siu, K. Venkatesan, K. Muhammad, J. B. H. Ng, L. Seet, E. Baptista, N. Escoval, A. Tomas, E. Agrawal, R. Mathew, R. Varma, A. Dima, E. Charitidou, E. Perivolioti, E. Pratikaki, M. Vrettou, C. Giannopoulos, A. Zakynthinos, S. Routsi, C. Atchade, E. Houzé, S. Jean-Baptiste, S. Thabut, G. Genève, C. Tanaka, S. Lortat-Jacob, B. Augustin, P. Desmard, M. Montravers, P. de Molina, F. J. González Barbadillo, S. Alejandro, R. Texas Children’s Hospital Clinical Nutriiton Houston USA Texas Children’s Hospital Intensive Care Houston USA Baylor College of Medicine Pediatrics Houston USA Kochi Medical School Department of Anesthesiology and Intensive Care Medicine Nankoku Japan Vall d’ Hebron University Hospital Critical Care Department Barcelona Spain Vall d’ Hebron University Hospital Anesthesia & Reanimation Department Barcelona Spain Vall d’ Hebron University Hospital Neurocritical Care Department Barcelona Spain Vall d’ Hebron University Hospital Coronary Care Unit Barcelona Spain Sagrat Cor University Hospital Critical Care Department Barcelona Spain St Elisabeth Twee Steden Hospital ICU Tilburg Netherlands National Institute of Cardiovascular Diseases PCICU Bratislava Slovakia National Institute of Cardiovascular Diseases Bratislava Slovakia National Institute of Cardiovascular Diseases Pediatric Cardiac Intensive Care Unit Bratislava Slovakia Texas Children’s Hospital Renal Service Houston USA Bristol Royal Hospital for Children Paediatric Intensive Care Unit Bristol UK Intensive Care National Audit & Research Centre (ICNARC) London UK University of Leeds Leeds UK Southampton University Hospitals NHS Trust Southampton UK Great Ormond Street Hospital London UK UCCC ICU Kyiv Ukraine Catholic University Department of Anesthesia and Intensive Care Rome Italy International Renal Research Institute of Vicenza (IRRIV) Department of Nephrology Dialysis and Transplantation Vicenza Italy University of Florence Department of Health Science Section of Anaesthesiology and Intensive Care Florence Italy The Children’s Hospital at Montefiore Pediatric Critical Care Bronx USA The Children’s Hospital at Montefiore Bronx USA Shiraz University of Medical Sciences Pediatric intensive Care Shiraz Islamic Republic of Iran Shiraz University of Medical Sciences Shiraz Islamic Republic of Iran Yokohama City University Hospital Intensive Care Unit Yokohama Japan Yokohama City Univ

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Development of tsunami evacuation simulation for Banda Aceh City planning

Development of tsunami evacuation simulation for Banda Aceh ...

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20th International Conference on Software engineering and Data engineering, SEDE 2011

作者： Affan, Muzailin Agussabti Goto, Yozo Abidin, Taufik Fuadi Koshimura, Shunichi Informatics Study Program Faculty of Sciences Syiah Kuala University Banda Aceh 23111 Indonesia Faculty of Agriculture Syiah Kuala University Banda Aceh 23111 Indonesia Earthquake Research Institute University of Tokyo Tokyo Japan Tsunami Engineering Laboratory Tohoku University Sendai Japan

ISBN: (纸本)9781880843826

The tsunami evacuation simulation which combines tsunami inundation simulation and people evacuation simulation was confirmed to be one of the effective disaster education tools from the experiences in Japan. This simulation technology has been advanced and applied to the west half of the tsunami risk area of Banda Aceh. And, its utilization methodology for tsunami disaster education and for city planning has been studied under the cooperation with the school teachers and the city office staffs. Linking these two simulations onto a common time-domain, the animation is compiled and the number of casualties is counted from the location of evacuee and the spot depth of tsunami. The study originated the road network data and population data of Banda Aceh using a high resolution satellite image and door-to-door visits. Several simulations were developed under different scenario parameters such as the timing of the start of evacuation, the method of moving (car is available or not), and the destination of the evacuees. The simulation handles more than 10 thousand agent models.

关键词： Tsunamis

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Simultaneous identification for synergistic transcription factors and their transcription factor binding sites

Simultaneous identification for synergistic transcription fa...

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5th International Conference on Complex, Intelligent and Software Intensive Systems, CISIS 2011

作者： Tsai, Zing Tsung-Yeh Huang, Grace Tzu-Wei Tsai, Huai-Kuang Institute of Information Science Academia Sinica Taipei 115 Taiwan Bioinformatics Program Taiwan International Graduate Program Taiwan Institute of Biomedical Informatics National Yang-Ming University Taiwan Joint CMU-Pitt PhD Program in Computational Biology University of Pittsburgh Carnegie Mellon University Pittsburgh PA United States Research Center for Information Technology Innovation Taipei 115 Taiwan Computer Science and Engineering National Taiwan Ocean University Keelung 202 Taiwan

ISBN: (纸本)9780769543734

Identifying transcription factor binding sites (TFBSs) is crucial for understanding the mechanism of transcriptional regulation. It is known that transcription factors (TFs) often cooperate to regulate genes. While traditional approaches can be used to discover binding motifs of a group of co-regulated genes, they often fail to accurately assign motifs to the corresponding TFs. Here, we consider two TFs together to infer their TFBSs and their synergistic relationship simultaneously. The basic idea is that if two TFs interact, their TFBSs, if distinct, would be conserved across species and coincided in the promoter regions of the genes they co-regulated. Applying our method to Saccharomyces cerevisiae chromatin immunoprecipitation data, we predicted 110 TF pairs with statistically significant motif assignments. A majority of these TF pairs have literature support to be synergistic, and the designated motifs to TFs match well with their known consensus. We further examined the synergism of predicted TF pairs in seven experimental conditions using ANOVA, and identified significant interactions. © 2011 IEEE.

关键词： Yeast

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