bluuebunny/crossref_metadata_2025_split huggingface dataset:
Introduction to bioinformatics
Authors: Fenstermacher David 
Published: January 2005

AbstractBioinformatics is a multifaceted discipline combining many scientific fields including computational biology, statistics, mathematics, molecular biology, and genetics. Bioinformatics enables biomedical investigators to exploit existing and emerging computational technologies to seamlessly store, mine, retrieve, and analyze data from genomics and proteomics technologies. This is achieved by creating unified data models, standardizing data interfaces, developing structured vocabularies, generating new data visualization methods, and capturing detailed metadata that describes various aspects of the experimental design and analysis methods. Already there are a number of related undertakings that are dividing the field into more specialized groups. Clinical Bioinformatics and Biomedical Informatics are emerging as transitional fields to promote the utilization of genomics and proteomics data combined with medical history and demographic data towards personalized medicine, molecular diagnostics, pharmacogenomics and predicting outcomes of therapeutic interventions. The field of bioinformatics will continue to evolve through the incorporation of diverse technologies and methodologies that draw experts from disparate fields to create the latest computational and informational tools specifically design for the biomedical research enterprise.
Information problems in molecular biology and bioinformatics
Authors: MacMullen W. John , Denn Sheila O. 
Published: January 2005

AbstractIn this article we provide an overview of opportunities for research and practice in the domain of molecular biology by information and library scientists. We introduce the changing role of data and information in molecular biology, and how molecular biology is evolving from a technique‐ and technology‐driven science to an information‐driven science. We then describe the high‐level objectives of molecular biology and some broad classes of problems from an information perspective. We illustrate the high‐level objectives with examples of specific tasks performed by biologists. Finally, we provide some programmatic direction for information and library science research streams and insertion points.
Integrated bioinformatics application for automated target discovery
Authors: Toldo Luca , Rippmann Friedrich 
Published: January 2005

AbstractIn this article we present an in silico method that automatically assigns putative functions to DNA sequences. The annotations are at an increasingly conceptual level, up to identifying general biomedical fields to which the sequences could contribute. This bioinformatics data‐mining system makes substantial use of several resources: a locally stored MEDLINE® database; a manually built classification system; the MeSH® taxonomy; relational technology; and bioinformatics methods. Knowledge is generated from various data sources by using well‐defined semantics, and by exploiting direct links between them. A two‐dimensional “Concept Map™” displays the knowledge graph, which allows causal connections to be followed. The use of this method has been valuable and has saved considerable time in our in‐house projects, and can be generally exploited for any sequence‐annotation or knowledge‐condensation task.
Mining association rules from biological databases
Authors: Rodríguez Andrés , Carazo José María , Trelles Oswaldo 
Published: January 2005

AbstractWe present a novel application of knowledge discovery technology to a developing and challenging application area such as bioinformatics. This methodology allows the identification of relationships between low‐magnitude similarity (LMS) sequence patterns and other well‐contrasted protein characteristics, such as those described by database annotations. We start with the identification of these signals inside protein sequences by exhaustive database searching and automatic pattern recognition strategies. In a second step we address the discovering of association rules that will allow tagging sequences that hold LMS signals with consequent functional keywords. We have designed our own algorithm for discovering association rules, meeting the special necessities of bioinformatics problems, where the patterns we search lie in sparse datasets and are uncommon and thus difficult to locate. Computational efficiency has been verified both with synthetic and real biological data showing that the algorithm is well suited to this application area compared to state of the art algorithms. The usefulness of the method is confirmed by its ability to produce previously unknown and useful knowledge in the area of biological sequence analysis. In addition, we introduce a new and promising application of the rule extraction algorithm on gene expression databases.
Reconfigurable Web wrapper agents for biological information integration
Authors: Hsu Chun‐Nan , Chang Chia‐Hui , Hsieh Chang‐Huain , Lu Jiann‐Jyh , Chang Chien‐Chi 
Published: January 2005

AbstractA variety of biological data is transferred and exchanged in overwhelming volumes on the World Wide Web. How to rapidly capture, utilize, and integrate the information on the Internet to discover valuable biological knowledge is one of the most critical issues in bioinformatics. Many information integration systems have been proposed for integrating biological data. These systems usually rely on an intermediate software layer called wrappers to access connected information sources. Wrapper construction for Web data sources is often specially hand coded to accommodate the differences between each Web site. However, programming a Web wrapper requires substantial programming skill, and is time‐consuming and hard to maintain. In this article we provide a solution for rapidly building software agents that can serve as Web wrappers for biological information integration. We define an XML‐based language called Web Navigation Description Language (WNDL), to model a Web‐browsing session. A WNDL script describes how to locate the data, extract the data, and combine the data. By executing different WNDL scripts, we can automate virtually all types of Web‐browsing sessions. We also describe IEPAD (Information Extraction Based on Pattern Discovery), a data extractor based on pattern discovery techniques. IEPAD allows our software agents to automatically discover the extraction rules to extract the contents of a structurally formatted Web page. With a programming‐by‐example authoring tool, a user can generate a complete Web wrapper agent by browsing the target Web sites. We built a variety of biological applications to demonstrate the feasibility of our approach.
Survey of bioinformatics programs in the United States
Authors: Hemminger Bradley M. , Losi Trish , Bauers Anne 
Published: January 2005

AbstractBioinformatics is a rapidly growing field, and educational programs for bioinformatics are increasing at a similar pace to answer the demand for qualified professionals. Here we survey currently available bioinformatics programs. We have compiled summaries of these programs, including university, state, degree type, department, entrance requirements, degree requirements, links to course Web pages, research interests, and funding. Complete details are presented in the Web version, and an abbreviated listing of the primary attributes of all programs is included in this article.
Extramural funding opportunities in bioinformatics from the National Library of Medicine
Authors: Bean Carol A. , Corn Milton 
Published: January 2005

AbstractNational Library of Medicine (NLM) extramural programs in bioinformatics are described in the context of National Institutes of Health (NIH) funding mechanisms and illustrated through a sampling of recently funded grants. The NIH application, evaluation, and funding process is described as used by the NLM.
Small nonphosphorylated Grb2–SH2 domain antagonists evaluated by surface plasmon resonance technology
Authors: Lung Feng‐Di T. , Chang Chiung‐Wen , Chong Meng‐Chin , Liou Chien‐Chung , Li Peng , Peach Megan L. , Nicklaus Marc C. , Lou Bih‐Show , Roller Peter P. 
Published: January 2005

AbstractThe growth factor receptor‐binding protein–Src homology 2 (Grb2–SH2) domain plays an important role in the oncogenic Ras signal transduction pathway, which involves cell proliferation and differentiation. Therefore, the Grb2–SH2 domain has been chosen as our target for development of potential antiproliferative agents. Herein, we report the study of the inhibitory effects of small nonphosphorylated peptide analogs interacting with the Grb2–SH2 domain protein by surface plasmon resonance (SPR) technology. A set of 8 related peptide analogs were synthesized, purified, and characterized. Their inhibitory effects on Grb2–SH2 were evaluated by the SPR technology developed with the BIACORE X instrument. The lead peptide, Fmoc–Glu–Tyr–Aib–Asn–NH2 (Fmoc–E–Y–Aib–N; Fmoc: 9‐fluorenylmethyoxycarbonyl; Aib = α‐amino isobutyric acid) inhibited Grb2–SH2 domain function with an IC50 value of 8.7 μM. A molecular modeling study of the lead peptide indicated that the glutamate in the Fmoc peptide is ideally positioned to form a strong salt bridge to Arg 67 in the Grb2–SH2 domain, using both its backbone carbonyl and its acidic group. Residue Glu 89 in Grb2–SH2 flips inward to fill the binding site and partially replace the phosphate group as a hydrogen‐bond acceptor. Results of these studies provide important information for further development of potent nonphosphorylated peptide inhibitors of the Grb2–SH2 domain. © 2005 Wiley Periodicals, Inc. Biopolymers (Pept Sci), 2005
Low‐loss wide‐angle Y‐branch optical waveguides
Authors: Yabu Tetsuro , Geshiro Masahiro , Ohashi Masaharu 
Published: January 2005

AbstractA new structure of a wide‐angle Y‐branch waveguide is proposed. In the proposed structure, only two kinds of materials are used and no sharp edge exists in the structure. Therefore, fabrication is easy and the practical value is high. In this study, numerical simulations are carried out by the beam propagation method using the ADI algorithm for the three‐dimensional structure. It is confirmed that the proposed structure shows excellent characteristics. Further, the applicability of the effective index method to the present branching structure is discussed. It is shown that the accuracy of the effective index method is not so high for the present structure. Therefore, three‐dimensional analysis is necessary for the present structure. © 2005 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 88(2): 11–18, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20122
Evaluation of trap states at front and back oxide interfaces and grain boundaries using electrical characteristic analysis and device simulation of polycrystalline silicon thin‐film transistors
Authors: Kimura Mutsumi 
Published: January 2005

AbstractThe trap states at the front and back oxide interfaces and grain boundaries of polycrystalline silicon thin‐film transistors are evaluated by using electrical characteristic analysis and device simulation. First, the method for extracting the trap densities of the front and back oxide interfaces and the grain boundaries is explained as the electrical characteristic analysis. When applied to the diagnosis of actual transistor characteristics, we see that oxygen plasma treatment or vapor heat treatment effectively decreases the trap densities at the front and back oxide interfaces, and self‐heating degradation increases the trap densities at the front and back oxide interfaces. Next, we use device simulation to examine the dependence of the transistor characteristics on the trap densities. When the simulation results were similarly applied to the diagnosis of actual transistor characteristics, we see that the oxygen plasma treatment naturally reduced the trap densities at the oxide interfaces, and the plasma‐enhanced chemical‐vapor deposition of tetraethylorthosilicate increased the trap densities at the grain boundaries. In a systematic summary of these analysis results, the effects of the trap states on the transistor characteristics, the improvement method, and the causes of degradation are discussed. © 2005 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 88(2): 1–10, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20124
Three‐dimensional numerical analysis on discharge properties of microwave excited ring dielectric line surface wave processing plasma device
Authors: Nakagawa Takashi , Kim Jaeho , Toba Takayuki , Katsurai Makoto 
Published: January 2005

AbstractA three‐dimensional simulation code with the finite difference time domain (FDTD) method combined with the electron fluid model has been developed for the microwave excited surface wave plasma in the RDL‐SWP device. This code permits the three‐dimensional numerical analysis of the spatial distributions of electric field, power absorption, electron density, and electron temperature. At a low gas pressure (about 10 mTorr), the numerical results were compared with the experimental measurements that show the validity of this 3D simulation code. A simplified analysis assuming that the electron density is spatially uniform has also been studied and its applicability is evaluated by the comparison of the 3D simulation and the analytical solutions. The surface wave eigenmodes are determined by the electron density, and it is found that the structure of the device strongly influences the spatial distribution of the electric fields of surface waves in a low‐density area (ne < 3.0 × 1011 cm−3). A method to irradiate by microwave the whole surface area of the plasma is proposed. The method is found to be effective in obtaining a high uniformity distribution of electron density. © 2005 Wiley Periodicals, Inc. Electr Eng Jpn, 150(4): 1–12, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.10333
Feasibility evaluation of on‐site generator network by cooperative game theory
Authors: Komiyama Ryoichi , Hayashi Taketo , Fujii Yasumasa , Yamaji Kenji 
Published: January 2005

AbstractAn on‐site generator, such as CGS (cogeneration system), is considered to be an effective end‐use energy system in order to accomplish primary energy conservation, CO2 emissions mitigation, and system cost reduction; these characteristics will eventually improve the complete performance of an existing energy system in the future. Considering the drawback of installing an end‐use CGS for a customer possessing small or middle‐scale floor space, however, it is difficult to achieve those distinctive features because the thermal‐electricity ratio of CGS is not always in agreement with that of customer energy demand. In order to overcome that matching deficiency, it is better to organize an on‐site generator network based on mutual electricity and heating transmission. But focusing on some cogenerators underlying their behaviors regarding maximizing their own profits, this on‐site network, whose situation corresponds to a grand coalition, is not necessarily established because of each cogenerator's motivation to form a partial coalition and acquire its own profit as much as possible.In this paper, we attempt to analyze the optimal operation of an on‐site generator network and identify by applying the nucleolus of cooperative game theory the optimal benefit allocation strategy in order for the cogenerators to construct the network. Regarding the installation site of this network, the center of Tokyo city is assumed; the locational information includes floor space and so forth through a GIS (geographic information system) database. The results from the nucleolus suggest that all districts should impartially obtain benefit from organizing the network for the purpose of jointly attaining system total cost reduction. © 2005 Wiley Periodicals, Inc. Electr Eng Jpn, 150(4): 23–35, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/eej.20052
Monomeric and polymeric anionic gemini surfactants and mixed surfactant systems in micellar electrokinetic chromatography. Part II: Characterization of chemical selectivity using two linear solvation energy relationship models
Authors: Akbay Cevdet , Agbaria Rezik A. , Warner Isiah M. 
Published: January 2005

AbstractSodium di(undecenyl) tartarate monomer (SDUT), a vesicle‐forming amphiphilic compound possessing two hydrophilic carboxylate headgroups and two hydrophobic undecenyl chains, was prepared and polymerized to form a polymeric vesicle (i.e., poly‐SDUT). The anionic surfactants of SDUT and poly‐SDUT (carboxylate head group) and sodium dodecyl sulfate, SDS (sulfate head groups) as well as mixed surfactant systems (SDS/SDUT, SDS/poly‐SDUT, and SDUT/poly‐SDUT) were applied as pseudostationary phases in micellar electrokinetic chromatography (MEKC). Two linear solvation energy relationship (LSER) models, i.e., solvatochromic and solvation parameter models, were successfully applied to investigate the effect of the type and composition of pseudostationary phases on the retention mechanism and selectivity in MEKC. The solvatochromic and solvation parameter models were used to help understand the fundamental nature of the solute‐pseudostationary phase interactions and to characterize the properties of the pseudostationary phases (e.g., solute size and hydrogen bond‐accepting ability for all pseudostationary phases). The solute types were found to have a significant effect on the LSER system coefficients and on the predicted retention factors. Although both LSER models provide the same information, the solvation parameter model is found to provide much better results both statistically and chemically than the solvatochromic model.
Analyte and system eigenpeaks in nonaqueous capillary zone electrophoresis: Theoretical description and experimental confirmation with methanol as solvent
Authors: Včeláková Kateřina , Zusková Iva , Porras Simo P. , Gaš Bohuslav , Kenndler Ernst 
Published: January 2005

AbstractA mathematical model developed for aqueous solutions and adapted to methanol as solvent was applied to predict the electromigration characteristics of analytes and background electrolytes in capillary zone electrophoresis. These characteristics are the effective mobility, and the tendency of the analyte to undergo peak‐broadening due to electromigration dispersion. The input parameters for calculation like limiting mobilities and dissociation constants were experimentally determined or taken from the literature. By the aid of the model, the molar response for conductivity detection was calculated as well as the transfer ratio when indirect UV detection was used. They allow depicting the electropherogram by computer simulation. An additional important program output is the prediction of the occurrence of system‐ or eigenpeaks that mimic peaks of analytes or electroosmotic flow markers. The measured electropherograms were in agreement with those theoretically predicted. Deviations were attributed to ion pairing in methanolic solutions, which was not implemented in the model.
Nanomaterials and chip‐based nanostructures for capillary electrophoretic separations of DNA
Authors: Lin Yang‐Wei , Huang Ming‐Feng , Chang Huan‐Tsung 
Published: January 2005

AbstractCapillary electrophoresis (CE) and microchip capillary electrophoresis (MCE) using polymer solutions are two of the most powerful techniques for the analysis of DNA. Problems, such as the difficulty of filling polymer solution to small separation channels, recovering DNA, and narrow separation size ranges, have put a pressure on developing new techniques for DNA analysis. In this review, we deal with DNA separation using chip‐based nanostructures and nanomaterials in CE and MCE. On the basis of the dependence of the mobility of DNA molecules on the size and shape of nanostructures, several unique chip‐based devices have been developed for the separation of DNA, particularly for long DNA molecules. Unlike conventional CE and MCE methods, sieving matrices are not required when using nanostructures. Filling extremely low‐viscosity nanomaterials in the presence and absence of polymer solutions to small separation channels is an alternative for the separations of DNA from several base pairs (bp) to tens kbp. The advantages and shortages of the use of nanostructured devices and nanomaterials for DNA separation are carefully addressed with respect to speed, resolution, reproducibility, costs, and operation.
Prefractionation techniques in proteome analysis: The mining tools of the third millennium
Authors: Righetti Pier Giorgio , Castagna Annalisa , Antonioli Paolo , Boschetti Egisto 
Published: January 2005

AbstractThe present review deals with prefractionation protocols used in proteomic investigation in preparation for mass spectrometry (MS) or two‐dimensional electrophoresis (2‐DE) map analysis. Briefly, reported methods focus on cell organelle differential centrifugation and on chromatographic approaches, to continue in extenso with a panoply of electrophoretic methods. In the case of chromatography, procedures useful as a prefractionation step, including affinity, ion‐exchange, and reversed‐phase resins, revealed several hundreds of new species, previously undetected in unfractionated samples. Novel chromatographic prefractionation methods are also discussed such as a multistaged fractionation column, consisting in a set of immobilized chemistries, serially connected in a stack format (an assembly of seven blocks), each capable of harvesting a given protein population. Such a method significantly simplifies the complexity of treated samples while concentrating species, all resulting in a larger number of visible proteins by MS or 2‐DE. Electrophoretic prefractionation protocols include all those electrokinetic methodologies which are performed in free solution, essentially all relying on isoelectric focusing steps (although some approaches based on gels and granulated media are also discussed). Devices associated with electrophoretic separation are multichamber apparatus, such as the multicompartment electrolyzers equipped with either isoelectric membranes or with isoelectric beads. Multicup device electrophoresis and several others, exploiting the conventional technique of carrier ampholyte focusing, are reviewed. This review also reports approaches for sample treatments in order to detect low‐abundance species. Among others, a special emphasis is made on the reduction of concentration difference between proteins constituting a sample. This latter consists in a library of combinatorial ligands coupled to small beads. Such a library comprises hexameric ligands composed of 20 amino acids, resulting in millions of different structures. When these beads are impregnated with complex proteomes (e.g., human sera) of widely differing protein compositions, they are able to significantly reduce the concentration differences, thus greatly enhancing the possibility to evidence low‐abundance species. It is felt that this panoply of methods could offer a strong step forward in “mining below the tip of the iceberg” for detecting the “unseen proteome”.