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作者： Kolasa, Marta Dlugosz, Rafal Jóźwicki, Wojciech Pauk, Jolanta Świetlicka, Aleksandra Farine, Pierre-André University of Technology and Life Sciences ul. Kaliskiego 7 85-796 Bydgoszcz Poland Institute of Microtechnology A.L.Breguet 2 CH- 2000 Neuchâtel Switzerland Nicolaus Copernicus University The Ludwik Rydygier Collegium Medicum Department of Pathology The Franciszek Lukaszczyk Oncology Center ul. Jagiellońska 13-15 85-067 Bydgoszcz Poland Bialystok University of Technology Wiejska St. 45C 15-351 Bialystok Poland Poznań University of Technology Chair of Computer Science Polanka 3A 60-965 Poznań Poland

ISBN: (纸本)9783037856451

This study presents a new approach to determine significant prognostic factors for patients suffering from the bladder cancer. The analysis of medical data has been performed by the use of the Kohonen self-organizing map (SOM). The SOM allows visualizing and identifying the prognostic factors indicating which of them are significant. A database comprised of ninety patients has been used in this study. Seven predictors were investigated. The cluster analysis indicates that the significant prognostic factors for the bladder cancer are: histological grade (cG) and stage (cT). The obtained results also showed that the sex and the cG variables are highly correlated and that the number of non-classic differentiation (NDNc) features in bladder cancer is somewhat correlated to surgically removed lymphnode number (LN) and metastatic positive lymphnode number (PLN). © (2013) Trans Tech Publications, Switzerland.

关键词： Self organizing maps

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A Robust Doppler Imaging Method Using Log-step Multicarrier Ultrasonic Signals

A Robust Doppler Imaging Method Using Log-step Multicarrier ...

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IEEE International Ultrasonics Symposium

作者： Yasushige Maeda Masanori Sugimoto Hiromichi Hashizume The Graduate University for Advanced Studies Department of Informatics School of Multidisciplinary Sciences 2-1-2 Hitotsubashi Chiyoda-ku Tokyo Japan Hokkaido University Department of Computer Science Kita-14 Nishi-9 Kita-ku Sapporo Japan National Institute of Informatics Information Systems Architecture Science Research Division 2-1-2 Hitotsubashi Chiyoda-ku Tokyo Japan

ISBN: (纸本)9781467356855

Recently, the authors described a new algorithm for ultrasonic Doppler imaging and velocity estimation using log-step multicarrier signals. The algorithm achieved a velocity estimation precision that was some 20 times better than that using an existing method, but the problem of estimation deficiency in low-SNR conditions remained. In this work, we improve the availability of the algorithm in low-SNR conditions by utilizing the systematic temporal shift of the log-step multicarrier signals, which expresses approximately the amount of Doppler shift in the sensed signal. A computer simulation shows high availability for the algorithm, even for SNR values below -10 dB.

关键词： authors algorithm sensed Writers Doppler effect Speed Estimation algorithms ultrasonic signal high availability signals computer Simulation Imaging Doppler Ultrasonography low SNR

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Layout-oblivious optimization for matrix computations 12

Layout-oblivious optimization for matrix computations

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21st International Conference on Parallel architectures and Compilation Techniques, PACT 2012

作者： Cui, Huimin Yi, Qing Xue, Jingling Feng, Xiaobing Institute of Computing Technology SKL Computer Architecture CAS Beijing China Depart. of Computer Science University of Texas at San Antonio San Antonio TX United States School of Computer Science and Engineering University of New South Wales Sydney NSW Australia

ISBN: (纸本)9781450311823

Most scientific computations serve to apply mathematical operations to a set of preconceived data structures, e.g., matrices, vectors, and grids. In this paper, we use a number of widely used matrix computations from the LINPACK library to demonstrate that complex internal organizations of data structures can severely degrade the effectiveness of compilers optimizations. We then present a data layout oblivious optimization methodology, where by isolating an abstract representation of computations from complex implementation details of their data, we enable these computations to be much more accurately analyzed and optimized through varying state-of-the-art compiler technologies. Copyright © 2012 by the Association for Computing Machinery, Inc. (ACM).

关键词： Data structures

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Mechanisms of Small RNA Generation from Cis-NATs in Response to Environmental and Developmental Cues

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Molecular Plant 2013年第3期6卷 704-715页

作者： Xiaoming Zhang Yifan Lii Zhigang Wu Anton Polishko Huiming Zhang Viswanathan Chinnusamy Stefano Lonardi Jian-Kang Zhu Renyi Liu Hailing Jin Department of Plant Pathology and Microbiology Center for Plant Cell Biology and Institute for Integrative Genome Biology University of California Riverside CA 92521 USA Department of Botany and Plant Sciences and Institute for Integrative Genome Biology University of California Riverside CA 92521 USA Computer Science and Engineering Center for Plant Cell Biology and Institute for Integrative Genome Biology University of California Riverside CA 92521 USA Department of Horticulture and Landscape Architecture Purdue University West Lafayette IN 47907 USA Division of Plant Physiology Indian Agricultural Research Institute New Delhi 110012 India Shanghai Center for Plant Stress Biology and Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China

ABSTRACT A large proportion of eukaryotic genomes is tranScribed from both positive and negative strands of DNA and thus may generate overlapping sense and antisense transcripts. Some of these so-called natural antisense transcripts （NATs） are possibly co-regulated. When the overlapping sense and antisense transcripts are expressed at the same time in the same cell in response to various developmental and environmental cues; they may form double-stranded RNAs, which could be recognized by the small RNA biogenesis machinery and processed into small interfering RNAs （siRNAs）. cis-NAT-derived siRNAs （nat-siRNAs） are present in plants, animals, and fungi. In plants, the presence of nat-siRNAs is supported not only by Northern blot and genetic analyses, but also by the fact that there is an overall sixfold enrichment of siRNAs in the overlapping regions of cis-NATs and 19%-29% of the siRNA-generating cis-NATs in plants give rise to siRNAs only in their overlapping regions. Silencing mediated by nat-siRNAs is one of the mechanisms for regulating the expression of the cis-NATs. This review focuses on challenging issues related to the biogenesis mechanisms as well as regulation and detection of nat-siRNAs. The advantages and limitations of new technologies for detecting cis-NATs, including direct RNA sequencing and strand-specific RNA sequencing, are also discussed.

关键词： gene expression gene regulation gene silencing.

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Akers's wavefront planner — One of the fastest stencil-based path planners on FPGAs

Akers's wavefront planner — One of the fastest stencil-base...

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International Conference on Reconfigurable Computing and FPGAs (ReConFig)

作者： Michael Schmidt Dietmar Fey Department Computer Science Chair of Computer Architecture Friedrich-Alexander-Universitat Erlangen-Nuremberg Germany

The efficient and fast processing of path planning algorithms based on stencil codes is a great challenge. On the one hand, these iterative approaches are advantageous because of their regular processing pattern and the characteristic to avoid problems of other path planning methods, like local minima in potential field algorithms. On the other hand, they are computational- and data-intensive because of their high number of required iterations. By comparing several algorithms based on stencil codes, we found one of the fastest and most efficient path planners for realization on FPGAs, Akers's wavefront planner. A processing of 33 maps per second with a resolution of 1024×1024 is possible on a midsize Virtex-5 FPGA achieved through a column-based processing scheme combined with an efficient internal data storage.

关键词： computer architecture Microprocessors Field programmable gate arrays Path planning Clocks Registers Robots

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Extendable pattern-oriented optimization directives

Extendable pattern-oriented optimization directives

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作者： Cui, Huimin Xue, Jingling Wang, Lei Yang, Yang Feng, Xiaobing Fan, Dongrui Key Laboratory of Computer System and Architecture Chinese Academy of Sciences Institute of Computing Technology Beijing China School of Computer Science and Engineering University of New South Wales Sydney NSW Australia

Algorithm-specific, that is, semantic-specific optimizations have been observed to bring significant performance gains, especially for a diverse set of multi/many-core architectures. However, current programming models and compiler technologies for the state-of-the-art architectures do not exploit well these performance opportunities. In this article, we propose a pattern-making methodology that enables algorithm-specific optimizations to be encapsulated into "optimization patterns". Such optimization patterns are expressed in terms of preprocessor directives so that simple annotations can result in significant performance improvements. To validate this new methodology, a framework, named EPOD, is developed to map these directives into the underlying optimization schemes for a particular architecture. It is difficult to create an exact performance model to determine an optimal or near-optimal optimization scheme (including which optimizations to apply and in which order) for a specific application, due to the complexity of applications and architectures. However, it is trackable to build individual optimization components and let compiler developers synthesize an optimization scheme from these components. Therefore, our EPOD framework provides an Optimization Programming Interface (OPI) for compiler developers to define new optimization schemes. Thus, new patterns can be integrated into EPOD in a flexible manner. We have identified and implemented a number of optimization patterns for three representative computer platforms. Our experimental results show that a pattern-guided compiler can outperform the state-of-theart compilers and even achieve performance as competitive as hand-tuned code. Therefore, such a patternmaking methodology represents an encouraging direction for domain experts' experience and knowledge to be integrated into general-purpose compilers. © 2012 ACM.

关键词： Semantics

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A speed-up study for a parallelized white light interferometry preprocessing algorithm on a virtual embedded multiprocessor system

A speed-up study for a parallelized white light interferomet...

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International Conference on architecture of Computing Systems (ARCS)

作者： Dominik Schoenwetter Max Schneider Dietmar Fey Chair of Computer Science 3 (Computer Architecture) Friedrich-Alexander-University of Erlangen-Nuremberg Erlangen Germany

Parallel computing has been a niche for scientific research in academia for decades. However, as common industrial applications become more and more performance demanding and raising the clock frequency of conventional single-core systems is hardly an option due to reaching technological limitations, efficient use of (embedded) multi-core CPUs and many-core platforms has become imperative. 3D surface analysis of objects using the white light interferometry presents one of such challenging applications. The goal in this article is to get an impression which speed-up for an established and parallelized white light interferometry preprocessing algorithm, called Contrast Method, is possible on an embedded system that works without any operating system. Therefore, we decided to use a virtual environment that is able to simulate embedded multi-core as well as many-core systems and that enables running real application code on the designed system. The results show, that a significant speedup is possible when using a many-core platform, instead of a design that only implements one single core, if the algorithm is parallelized for getting full advantage of the many-core design. Furthermore, an acceptable absolute run time is achievable.

关键词： Program processors Optical interferometry Interference Hardware Algorithm design and analysis Synchronization Multicore processing

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Fault-tolerant middleware based on multistream pipeline for private storage services

Fault-tolerant middleware based on multistream pipeline for ...

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7th International Conference for Internet Technology and Secured Transactions, ICITST 2012

作者： Gonzalez, J.L. Sosa-Sosa, Victor Bergua, Borja Sanchez, Luis Miguel Carretero, Jesus Cd. Valles Institute of Technology Information Technology Laboratory Center of Research CINVESTAV Ciudad Victoria Mexico Computer Architecture and Technology Area Computer Science Department Universidad Carlos III Madrid Spain

ISBN: (纸本)9781908320087

This paper presents a fault-tolerant middleware for private storage services based on a client-server model. A client-side API split files into redundant chunks, which are encoded/decoded, anonymized, and distributed to different storage locations in parallel by using multistream pipeline. A chunk placement engine on the server-side API receives/delivers chunks from/to the client side API. In this model, the user preserves her files in-house and achieves data availability anytime from anywhere even in site failure scenarios while the organizations preserves the control of their storage resources. The experimental evaluation reveals the middleware can compensate the overhead produced on the client side by taking advantage of multiple cores commonly found in user's devices. The users observe that the middleware produces similar performance to the private and public file hosting systems tested in the evaluation. The organizations observe a significant reduction of work in their servers. In site disaster scenarios, the middleware yields even better performance than fault-tolerant online distributed solutions tested in the evaluation. © 2012 Infonomics Society.

关键词： Middleware

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Image retrieval in data stream using principle component analysis

Image retrieval in data stream using principle component ana...

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2012 2nd International Conference on Consumer Electronics, Communications and Networks, CECNet 2012

作者： Yan, Han-Bing Liu, Ya-Shu National Institute of Network and Information Security China National Computer Network Emergency Response Technical Team Coordination Center of China China Department of Computer Science Beijing University of Civil Engineering and Architecture China

ISBN: (纸本)9781457714153

Image Retrieval in Data Stream is becoming very important in recent years with the development of internet and the focus on information security. In Data Stream, image retrieval is different from the traditional image retrieval in that, it requires high efficiency and network adaptive ability, while the traditional image retrieval does not have such hard requirements. In this paper, we propose a novel approach to retrieval image in data stream using Principle Component Analysis(PCA). By subdividing image into several blocks and extracting image principle features, our method can retrieval image very efficiently, this meets the needs of wide band width network traffic. Because the natural character of PCA, our method can be adaptive to the network traffic by simply modify a few parameters by an automatic way. Our experiments show that our approach has high Recall Rate and very low False Positive Rate. © 2012 IEEE.

关键词： Image retrieval

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Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

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BMC genomics 2016年第6期17 Suppl 6卷 487页

作者： Jerry W. Shay Noriko Homma Ruyun Zhou Muhammad Imran Naseer Adeel G. Chaudhary Mohammed Al-Qahtani Nobutaka Hirokawa Maryam Goudarzi Albert J. Fornace Saleh Baeesa Deema Hussain Mohammed Bangash Fahad Alghamdi Hans-Juergen Schulten Angel Carracedo Ishaq Khan Hanadi Qashqari Nawal Madkhali Mohamad Saka Kulvinder S. Saini Awatif Jamal Jaudah Al-Maghrabi Adel Abuzenadah Adeel Chaudhary Mohammed Al Qahtani Ghazi Damanhouri Heba Alkhatabi Anne Goodeve Laura Crookes Nikolas Niksic Nicholas Beauchamp Adel M. Abuzenadah Jim Vaught Bruce Budowle Mourad Assidi Abdelbaset Buhmeida Leena Merdad Sudhir Kumar Sayaka Miura Karen Gomez Mahmood Rasool Ahmed Rebai Sajjad Karim Hend F. Nour Eldin Heba Abusamra Elham M. Alhathli Nada Salem Mohammed H. Al-Qahtani Hossam Faheem Ashok Agarwa Eberhard Nieschlag Joachim Wistuba Oliver S. Damm Mohd A. Beg Taha A. Abdel-Meguid Hisham A. Mosli Osama S. Bajouh Serdar Coskun Muhammad Abu-Elmagd Ashraf Dallol Sahar Hakamy Wejdan Al-Qahtani Asia Al-Harbi Shireen Hussain Burak Ozkosem Rick DuBois Safia S. Messaoudi Maryam T. Dandana Touhami Mahjoub Wassim Y. Almawi S. Abdalla M. Nabil Al-Aama Asmaa Elzawahry Tsuyoshi Takahashi Sachiyo Mimaki Eisaku Furukawa Rie Nakatsuka Isao Kurosaka Takahiko Nishigaki Hiromi Nakamura Satoshi Serada Tetsuji Naka Seiichi Hirota Tatsuhiro Shibata Katsuya Tsuchihara Toshirou Nishida Mamoru Kato Sajid Mehmood Naeem Mahmood Ashraf Awais Asif Muhammad Bilal Malik Siddique Mehmood Aadil Hussain Qazi Mohammad Sajid Jamal Mughees Uddin Siddiqui Mohammad A. Alzohairy Mohammad A. Al Karaawi Taoufik Nedjadi Heba Al-Khattabi Adel Al-Ammari Ahmed Al-Sayyad Hédia Zitouni Nozha Raguema Marwa Ben Ali Wided Malah Raja Lfalah Wassim Almawi Mohammed Elanbari Andrey Ptitsyn Sana Mahjoub Rabeb El Ghali Bechir Achour Nidhal Ben Amor Brahim N’siri Hamid Morjani Esam Azhar Vera Chayeb Maryam Dendena Hedia Zitouni Khedija Zouari-Limayem Bassem Refaat Ahmed M. Ashshi Sarah A. Batwa Hazem Ramadan Amal Awad Ahmed Ateya Adel Galal Ahmed El-Shemi Ahmad Ashshi Mohammed Basalamah Youjin Na Cha University of Texas Southwestern Medical Center Dallas USA Department of Cell Biology and Anatomy Graduate School of Medicine the University of Tokyo Tokyo Japan Center of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Department of Biochemistry and Molecular & Cellular Biology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Oncology Lombardi Comprehensive Cancer Center Georgetown University Washington USA Department of Radiation Medicine Lombardi Comprehensive Cancer Center Georgetown University Washington USA Center of Excellence in Genomic Medicine Research (CEGMR) King Abdulaziz University Jeddah Kingdom of Saudi Arabia King Fahd Medical Research Centre King Abdulaziz University Jeddah Saudi Arabia Centre of Excellence in Genomic Medicine Research King Abdulaziz University Jeddah Saudi Arabia Sheffield Diagnostic Genetic Service Sheffield Children’s NHS Foundation Trust Western Bank Sheffield UK Center of Innovations in Personalized Medicine King Abdulaziz University Jeddah Saudi Arabia President ISBER Editor-in-Chief Biopreservation & Biobanking ᅟ USA Institute of Applied Genetics Department of Molecular and Medical Genetics University of North Texas Health Science Center Fort Worth USA Department of Dental Public Health Faculty of Dentistry King Abdulaziz University Jeddah Saudi Arabia Institute for Genomics and Evolutionary Medicine Temple University Philadelphia USA Center of Excellence in Genomic Medicine King Abdulaziz University Jeddah Kingdom of Saudi Arabia Laboratory of Molecular and Cellular Screening Processes (Bioinformatics Group) Centre of Biotechnology of Sfax Sfax Tunisia Fujitsu Technology Solutions International ᅟ ᅟ Case Western Reserve University School of Medicine and Lerner College of Medicine Cleveland Clinic Foundation Cleveland USA American Center for Reproductive Medicine Andrology Center Cleveland USA Center for Reproductive Medicine and

O1 Regulation of genes by telomere length over long distances Jerry W. Shay O2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsy Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa O3 Integration of metagenomics and metabolomics in gut microbiome research Maryam Goudarzi, Albert J. Fornace Jr. O4 A unique integrated system to discern pathogenesis of central nervous system tumors Saleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi Damanhouri O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis Heba Alkhatabi O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp O7 Targeted sequencing panels and their utilization in personalized medicine Adel M. Abuzenadah O8 International biobanking in the era of precision medicine Jim Vaught O9 Biobank and biodata for clinical and forensic applications Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors Jaudah Al-Maghrabi O11 The CEGMR biobanking unit: achievements, challenges and future plans Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad O12 Phylomedicine of tumors Sudhir Kumar, Sayaka Miura, Karen Gomez O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment Angel Carracedo, Mahmood Rasool O14 From association to causality: translation of GWAS findings for genomic me

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