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Decision fusion of circulating markers for breast cancer detection in premenopausal women

Decision fusion of circulating markers for breast cancer det...

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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Jesneck, Jonathan L. Mukherjee, Sayan Nolte, Loren W. Lokshin, Anna E. Marks, Jeffrey R. Lo, Joseph Department of Biomedical Engineering Department of Statistical Science Computational Biology and Bioinformatics Program Duke Advanced Imaging Labs. Institute for Genome Sciences and Policy Department of Computer Science Duke University Department of Electrical and Computer Engineering Division of Hematology/Oncology University of Pittsburgh School of Medicine University of Pittsburgh Cancer Institute Pittsburgh PA 15213 United States Department of Experimental Surgery Duke University Medical Center Medical Physics Graduate Program Duke University Durham NC 27708 United States

ISBN: (纸本)1424415098

Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Because the data set was very noisy and contained only weak features, we used a classifier designed for noisy data: decision fusion. Decision fusion outperformed both a support vector machine (SVM) and linear regression with forward stepwise feature selection on all three two-class classification tasks: normal tissue vs. cancer, normal tissue vs. benign lesions, and benign lesions vs. cancer. Decision fusion detected cancer moderately well (AUC=0.84 on normal vs. cancer), demonstrating promise as a screening tool. Decision fusion also detected benign lesions similarly well (AUC=0.83 on normal vs. benign lesions) and was the only classifier to achieve any success in separating benign from malignant lesions (AUC=0.64 on benign vs. cancer). The classification results suggest that the assayed proteins are more indicative of a secondary effect, such as immune response, rather than specific for breast cancer. In conclusion, the decision fusion classifier demonstrated some promise in detecting breast lesions and outperformed other classifiers, especially for the very noisy classification problem of distinguishing benign from malignant lesions. ©2007 IEEE.

关键词： Tissue

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Design and Evaluation of a Grid Computing Based Architecture for Integrating Heterogeneous IDSs

Design and Evaluation of a Grid Computing Based Architecture...

引用

IEEE GLOBECOM 2007 - IEEE Global Telecommunications Conference

作者： Paulo F. Silva Carlos B. Westphall Carla M. Westphall Marcos Dias de Assuncao Network and Management Laboratory Post-Graduate Program in Computer Science Federal University of Santa Catarina Florianopolis Brazil Grid Computing and Distributed Systems Laboratory Department of Computer Science and Software Engineering University of Melbourne VIC Australia

Intrusion detection systems (IDSs) have been substantially improved in recent past. However, network attacks have become more sophisticated and increasingly complex: many of current attacks are coordinated and originated in multiple networks. To detect these attacks, IDSs need to obtain information on network events from multiple networks or administrative domains. This work demonstrates that a Distributed IDS (DIDS) can be composed of existing IDSs, improving the detection of misuses in a multiple network environment. We use a grid middleware for creating a service-based intrusion detection grid. We demonstrate through experimental results that the proposed DIDS allows the integration of heterogeneous existing IDSs and improves the detection of attacks by exploring the synergy between existing IDSs.

关键词： Grid computing computer architecture Intrusion detection Resource management Laboratories computer science Electronic mail Middleware computer network management Engineering management

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Non-Crosshybridizing Oligonucleotide Building Blocks for Accurate, Scalable Nanofabrication

Non-Crosshybridizing Oligonucleotide Building Blocks for Acc...

引用

IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS)

作者： Jin-woo Kim Ju Seok Lee Russell Deaton Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR USA IEEE Senior Member Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR 72701 USA. Department of Computer Science and Computer Engineering University of Arkansas Fayetteville AR 72701 USA.

The urgent need in the field of nanotechnology is functional, reliable, and scalable techniques for more complicated and controlled nanostructures in order to realize nanoscale materials and devices that have practical use and more capability than existing technologies. This paper addresses this need by presenting an in vitro protocol to select large non-crosshybridizing (NCH) libraries of oligonucleotides that provide a large address space of DNA sequences with which to increase both complexity and control in DNA-directed self-assembly processes. The selection protocol was experimentally verified and confirmed. The resultant large NCH libraries would allow self-assembling complex nanostructures with more precise control, leading to reliable, scaled-up, cost-effective manufacturing of nanoscale devices and systems.

关键词： Nanofabrication Nanostructures Nanostructured materials Nanoscale devices Space technology Protocols Libraries Self-assembly Nanotechnology Materials reliability

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Use mathematics and computer to predict Boat's drift for search and rescue

Use mathematics and computer to predict Boat's drift for sea...

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International Multi-Conference on Society, Cybernetics and Informatics, IMSCI 2007

作者： Han, Jim Su, Hui Fang Huang Su, Tsung-Chow Joe Dept. of Computer Engineering and Computer Science Florida Atlantic University Boca Raton FL 33431 United States Graduate Teacher Education Program Nova Southeastern University 1750 NE 167th St. North Miami Beach FL 33162 United States Dept. of Mechanical Engineering Florida Atlantic University Boca Raton FL 33431 United States

ISBN: (纸本)1934272256

Finding a boat in wind and current is an age old problem that puzzled many people throughout history. It is only until recently a simple theory is developed to allow efficient and accurate prediction of the boat's drift trajectory. Such theory could be developed using simple physics and algebra. In this paper, we will describe the derivation of the theory that would give the boat's trajectory in terms of different types of boat condition under given wind field and current field. We will show that the relationship is versatile, and could be used for practical application. We will further implement the results in computer animation setting so that the results can be obtained easily for a given application. The paper demonstrates the power of mathematics and technology to solve problem of boat drift of search and rescue.

关键词： Boats

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Structural characterization of RNA-binding sites of proteins: Preliminary results

Structural characterization of RNA-binding sites of proteins...

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IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)

作者： Fadi Towfic David C. Gemperline Cornelia Caragea Feihong Wu Drena Dobbs Vasant Honavar Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA Department of Biology Department of Chemistry Carthage College Kenosha WI USA Department of Computer Science Iowa State University Ames IA USA Department of Genetics Development and Cell Biology Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA Department of Computer Science Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA

We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc), using a non-redundant dataset of 147 protein chains extracted from protein-RNA complexes in the protein data bank. Our analysis of surface roughness, solid angle and CX value of amino acid residues for each of the protein chains in the dataset shows that: The protein-RNA interface residues tend to be protruding compared to non-interface residues and tend to have higher surface roughness and exhibit moderately convex or concave solid angles. Furthermore, the protein chains in protein-RNA interfaces that contain Viral RNA and rRNA significantly differ from those that contain dsRNA, mRNA siRNA, snRNA, SRP RNA and tRNA with respect to their CX values. The results of this analysis sug gests the possibility of using such structural features to reliably identify protein-RNA interface residues when the structure of the protein is available but the structures of complexes formed by the protein with RNA are not.

关键词： RNA Protein engineering Biology computing Amino acids Bioinformatics computer interfaces Rough surfaces Surface roughness Solids Machine learning

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Interpreting cabinet approval ratings by neural networks

Interpreting cabinet approval ratings by neural networks

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IASTED International Conference on Artificial Intelligence and Applications, AIA 2007

作者： Kamimura, Ryotaro Yoshida, Fumihiko Kitajima, Ryozo Information Science Laboratory Information Technology Center Tokai University 1117 Kitakaname Hiratsuka Kanagawa 259-1292 Japan Department of Media Studies Tokai University 1117 Kitakaname Hiratsuka Kanagawa 259-1292 Japan Graduate Program in Computer Sciences Tokai University 1117 Kitakaname Hiratsuka Kanagawa 259-1292 Japan

ISBN: (纸本)9780889866317

In this paper, we try to estimate Japan's cabinet approval ratings by using neural networks. In addition, we try to extract the important features in input patterns. This is the first attempt to use neural networks and to interpret the mechanism of inference for approval estimation in a comprehensive way. Experimental results show that neural networks have much better performance than that obtained by the standard regression analysis in terms of training and testing errors. The information loss analysis reveals that the first variable, that is, the previous ratings should play the most important role in inference. Though the experimental result here shown is a preliminary one, it certainly suggests a possibility of the automatic inference of cabinet approval ratings.

关键词： Feature extraction

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Evolving hypernetwork classifiers for microRNA expression profile analysis

Evolving hypernetwork classifiers for microRNA expression pr...

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Congress on Evolutionary Computation

作者： Sun Kim Soo-Jin Kim Byoung-Tak Zhang The Center for Bioinformatics Technology Graduate Program in Bioinformatics Seoul National University Seoul South Korea The School of Computer Science and Engineering Seoul National University Seoul South Korea

High-throughput microarrays inform us on different outlooks of the molecular mechanisms underlying the function of cells and organisms. While computational analysis for the microarrays show good performance, it is still difficult to infer modules of multiple co-regulated genes. Here, we present a novel classification method to identify the gene modules associated with cancers from microarray data. The proposed approach is based on 'hypernetworks', a hypergraph model consisting of vertices and weighted hyperedges. The hypernetwork model is inspired by biological networks and its learning process is suitable for identifying interacting gene modules. Applied to the analysis of microRNA (miRNA) expression profiles on multiple human cancers, the hypernetwork classifiers identified cancer-related miRNA modules. The results show that our method performs better than decision trees and naive Bayes. The biological meaning of the discovered miRNA modules has been examined by literature search.

关键词： Cancer Gene expression Biological system modeling Data analysis Support vector machines Support vector machine classification Evolutionary computation Humans Decision trees Diseases

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DNA-Directed Self-Assembly of Microscopic 1-D Carbon Nanotube Wire

DNA-Directed Self-Assembly of Microscopic 1-D Carbon Nanotub...

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IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS)

作者： Jin-Woo Kim Nalinikanth Kotagiri Russell Deaton Steve Tung Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR USA IEEE Senior Member Cell and Molecular Biology Graduate Program University of Arkansas Fayetteville AR 72701 USA. Department of Computer Science and Computer Engineering University of Arkansas Fayetteville AR 72701 USA. Department of Mechanical Engineering University of Arkansas Fayetteville AR USA

Molecular wire construction using DNA-directed self-assembly of multi-walled carbon nanotubes (MWNTs) has been attempted. MWNTs were selected owing to their exceptional electrical and structural properties. DNA, which possesses specific molecular recognition properties, served as the engine for the assembly. Non-crosshybridizing (NCH) sequences were designed to impart specificity and high throughput reaction. Stepwise manufacturing of the wire was accomplished by first functionalizing the NCH 20 base pair single-stranded sequences to the tips of MWNT using amide linkage. The adducts were then utilized to self-assemble 1D nanotube wire through DNA hybridization reactions between two complementary ssDNAs functionalized to the MWNT tips. TEM, epi-fluorescent microscopy and AFM analyses showed successful assemblies of micrometer-scale 1D MWNT-DNA wires, ranging from 2.7-20 mum. The results demonstrate great potentials of the DNA-guided self-assembly process, which would provide an uncomplicated, versatile and inexpensive way to manufacture micrometer-scale molecular wires.

关键词： Self-assembly Carbon nanotubes Wire Atomic force microscopy Transmission electron microscopy DNA Assembly Sequences Engines Throughput

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Information-Theoretic Variable Selection in Neural Networks

Information-Theoretic Variable Selection in Neural Networks

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IEEE Symposium on Foundations of Computational Intelligence, FOCI

作者： Ryotaro Kamimura Fumihiko Yoshida Yamashita Toshie Ryozo Kitajima Information Technology Center Information Science Laboratory Japan Department of Media Studies Tokai University Hiratsuka Kanagawa Japan Graduate Program in Computer Sciences Tokai University Hiratsuka Kanagawa Japan

In this paper, we propose a new type of information-theoretic approach to variable selection. Many approaches have been proposed in estimating the importance of input variables. The majority of these approaches have focused upon output errors. We here introduce an approach concerning internal representations. First, we delete an input unit with corresponding connection weights. Then, by examining some change in hidden unit activation with and without a input variable, we can extract an important variable. We apply this method to an artificial data in which the number of hidden units is redundantly increased so as to clearly show improved performance and the stability of our method. Then, we apply the method to the cabinet approval ratings in which better interpretation of input variables can be given

关键词： Input variables Neural networks Computational intelligence computer networks Information theory Data mining Standards development Measurement units Information science Laboratories

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AC 2007-1771: Mentoring new faculty: How much, how often, and how?

AC 2007-1771: Mentoring new faculty: How much, how often, an...

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114th Annual ASEE Conference and Exposition, 2007

作者： Jackson, Andrew Chin, Robert Coddington, Charles Petersen, Paul Hamid, Fonooni East Carolina University United States Department of Technology Systems College of Technology and Computer Science East Carolina University United States East Carolina University Indiana State University Graduate Faculties United States EDGJ Department of Technology Systems East Carolina University United States Faculty Senate East Carolina University United States Department of Technology East Carolina University College of Technology and Computer Science United States Cleveland State University Fenn College of Engineering United States Department of Technology Systems Science Occupational Safety Program East Carolina University Greenville NC United States Academic Practice Specialty Educational Standards Committee Task Force ASSE

The Department of Technology Systems (TSYS) at East Carolina University has implemented a new faculty mentoring process to enable junior faculty members to learn from senior faculty members as they prepare for a career in academia. Five tenured professors and associate professors in the TSYS department have recently established a new process to mentor faculty members within the department who have begun not yet completed their initial tenure process at a major university. This process includes a series of workshops regarding academic performance expectations during the early stages of an academic career. Our commitment to new faculty takes on several related, yet distinct features. Examples of these initiatives include: 1) reduced workloads for new faculty for the first two years to enable them to generate individual and collaborative research activities, funded grants, and publications, 2) periodic university-wide training to learn policies and procedures that affect day-to-day activities on a college campus, 3) periodic workshops hosted by senior faculty mentors, and 4) one-on-one discussions between senior faculty members and junior faculty members to encourage candid dialogue between professional colleagues. Another feature of the mentorship philosophy is a proposal to the dean of the college to offer newly hired faculty a contractual start date of July 1steach year instead of starting their contract one week prior to the start of fall classes, normally in late August. This additional period of time will be used to train new faculty in essential policies and procedures, to complete a variety of administrative tasks on campus, to get a head start on preparing for classes in the fall, and cleaning up those supplemental tasks that accompany every move to a new location. The goal of this early commitment to new faculty is to reduce the stress associated with preparing for a new course, in a new environment, with a new set of operating procedures. This will also enab

关键词： Engineering education

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