bluuebunny/crossref_metadata_2025 huggingface dataset:
TRIP6 is a RIP2-associated common signaling component of multiple NF-κB activation pathways
Authors: Li Lianyun , Bin Liang-Hua , Li Fu , Liu Yi , Chen Danying , Zhai Zhonghe , Shu Hong-Bing
Published: January 2005

Receptor-interacting protein 2 (RIP2) is a member of the RIP kinase family that has been shown to be crucially involved in inflammation, innate and adaptive immune responses. The physiological and pathological roles of RIP2 are mediated through its involvement in multiple NF-κB activation pathways, including those triggered by tumor necrosis factor (TNF), interleukin 1 (IL-1), Toll-like receptor 2 (TLR2), TLR3, TLR4 and Nod1. In this report, we identified the LIM-domain-containing protein TRIP6 as a RIP2-interacting protein in yeast two-hybrid screens. In mammalian cells, TRIP6 interacts with RIP2 in a TNF- or IL-1-dependent manner. Overexpression of TRIP6 potentiates RIP2-mediated NF-κB activation in a dose-dependent manner. The LIM domains of TRIP6 are responsible for its interaction with RIP2. TRIP6 also interacts with TRAF2, a protein that is crucially involved in TNF signaling, as well as the IL-1 receptor, TLR2 and Nod1. Overexpression of TRIP6 potentiates NF-κB activation by TNF, IL-1, TLR2 or Nod1, whereas a dominant negative mutant or RNA-interference construct of TRIP6 inhibits NF-κB activation by TNF, IL-1, TLR2 or Nod1. Moreover, TRIP6 also potentiates RIP2- and Nod1-mediated ERK activation. These data have established a physical and functional association between TRIP6 and RIP2, and suggest that RIP2's involvement in multiple NF-κB and ERK activation pathways is mediated through TRIP6.
Downregulation of Par3 and aPKC function directs cells towards the ICM in the preimplantation mouse embryo
Authors: Plusa Berenika , Frankenberg Stephen , Chalmers Andrew , Hadjantonakis Anna-Katerina , Moore Catherine A. , Papalopulu Nancy , Papaioannou Virginia E. , Glover David M. , Zernicka-Goetz Magdalena
Published: January 2005

Generation of inside cells that develop into inner cell mass (ICM) and outside cells that develop into trophectoderm is central to the development of the early mouse embryo. Critical to this decision is the development of cell polarity and the associated asymmetric (differentiative) divisions of the 8-cell-stage blastomeres. The underlying molecular mechanisms for these events are not understood. As the Par3/aPKC complex has a role in establishing cellular polarity and division orientation in other systems, we explored its potential function in the developing mouse embryo. We show that both Par3 and aPKC adopt a polarized localization from the 8-cell stage onwards and that manipulating their function re-directs cell positioning and consequently influences cell fate. Injection of dsRNA against Par3 or mRNA for a dominant negative form of aPKC into a random blastomere at the 4-cell stage directs progeny of the injected cell into the inside part of the embryo. This appears to result from both an increased frequency by which such cells undertake differentiative divisions and their decreased probability of retaining outside positions. Thus, the natural spatial allocation of blastomere progeny can be over-ridden by downregulation of Par3 or aPKC, leading to a deceased tendency for them to remain outside and so develop into trophectoderm. In addition, this experimental approach illustrates a powerful means of manipulating gene expression in a specific clonal population of cells in the preimplantation embryo.
Characterization of a native hammerhead ribozyme derived from schistosomes
Authors: OSBORNE EDITH M. , SCHAAK JANELL E. , DEROSE VICTORIA J.
Published: January 2005

A recent re-examination of the role of the helices surrounding the conserved core of the hammerhead ribozyme has identified putative loop–loop interactions between stems I and II in native hammerhead sequences. These extended hammerhead sequences are more active at low concentrations of divalent cations than are minimal hammerheads. The loop–loop interactions are proposed to stabilize a more active conformation of the conserved core. Here, a kinetic and thermodynamic characterization of an extended hammerhead sequence derived from Schistosoma mansoni is performed. Biphasic kinetics are observed, suggesting the presence of at least two conformers, one cleaving with a fast rate and the other with a slow rate. Replacing loop II with a poly(U) sequence designed to eliminate the interaction between the two loops results in greatly diminished activity, suggesting that the loop–loop interactions do aid in forming a more active conformation. Previous studies with minimal hammerheads have shown deleterious effects of Rp-phosphorothioate substitutions at the cleavage site and 5′ to A9, both of which could be rescued with Cd2+. Here, phosphorothioate modifications at the cleavage site and 5′ to A9 were made in the schistosome-derived sequence. In Mg2+, both phosphorothioate substitutions decreased the overall fraction cleaved without significantly affecting the observed rate of cleavage. The addition of Cd2+ rescued cleavage in both cases, suggesting that these are still putative metal binding sites in this native sequence.
Autobiography and narrative in personal development planning in the creative arts
Authors: James Alison
Published: January 2005

Personal development planning (PDP) is being promoted to enable students to examine their practices, beliefs, behaviours and achievements in the fullest context of their learning. This article will summarize developments to date with progress files, consider what PDP is, including the
tension between its external, sociocultural role (the demonstration of skills and assets to others) and capacity to enhance internal, individual understanding. The special contribution made by creative arts education in shaping PDP will be explored. Ambivalence in the sector as to both PDP
and writing will be considered in the light of experiments with alternative writing practices. In particular, these will relate to the emergence of personal narrative and authorial voice, detectable in both the visual product and the learning process. Drawing on my research into autobiography
and PDP I will propose a two-tier narrative framework for PDP that can be both motivating for the learner and productive as a metacognitive tool.
We have a lot to talk about: dialogue journals in graphic design education
Authors: Lawrie Samantha
Published: January 2005

This article describes continuing research into the role of dialogue journals within graphic design education. The application of dialogue journals described was developed as part of a seminar series on the history of graphic design and was designed to meet the needs of undergraduate
graphic design majors at a state-funded university in the south-eastern United States. Identified student needs, based on studio observations and on the students’ completion of a brief questionnaire, included a need to expand students’ conception of graphic design beyond a preoccupation
with computer software; a need for students to understand design activity within a broader cultural context than their own studio or personal life experiences; and a need for students to be verbally as well as visually literate within the discipline of graphic design. In this article I discuss
the theoretical rationale for using dialogue journals, an example of journal application within design education, a brief report of preliminary results, and suggestions for further study.
Writing Purposefully in Art and Design (Writing PAD)
Authors: Lockheart Julia , Edwards Harriet , Raein Maziar , Raatz Christoph
Published: January 2005

Why do students undertaking practice-based Art and Design (A&D) degree courses have to write? What kind of writing would support them best in their practice? How do we mark student writing that challenges our current writing criteria? The ‘Writing Purposefully in Art and Design’
(Writing PAD) project seeks to encourage debates around writing in A&D. This article details the first year of the project and lays out the various debates that have developed. The project was initiated to focus specifically on disseminating current good practice for students with visual-spatial
learning styles and dyslexia, international students, and mature students. This article presents the spectrum of views that have arisen from our discussions over the year. The issues presented are followed by the implications for change that have emerged from the various Writing PAD activities.
Correlation between Speed Perception and Neural Activity in the Middle Temporal Visual Area
Authors: Liu Jing , Newsome William T.
Published: January 2005

We conducted electrophysiological recording and microstimulation experiments to test the hypothesis that the middle temporal visual area (MT) plays a direct role in perception of the speed of moving visual stimuli. We trained rhesus monkeys on a speed discrimination task in which monkeys chose the faster speed of two moving random dot patterns presented simultaneously in spatially segregated apertures. In electrophysiological experiments, we analyzed the activity of speed-tuned MT neurons and multiunit clusters during the discrimination task. Neural activity was correlated with the monkeys' behavioral choices on a trial-to-trial basis (choice probability), and the correlation was predicted by the speed-tuning properties of each unit. In microstimulation experiments, we activated clusters of MT neurons with homogeneous speed-tuning properties during the same speed discrimination task. In one monkey, microstimulation biased speed judgments toward the preferred speed of the stimulated neurons. Together, evidence from these two experiments suggests that MT neurons play a direct role in the perception of visual speed. Comparison of psychometric and neurometric thresholds revealed that single and multineuronal signals were, on average, considerably less sensitive than were the monkeys perceptually, suggesting that signals must be pooled across neurons to account for performance.
Synaptic Targeting of Retrogradely Transported Trophic Factors in Motoneurons: Comparison of Glial Cell Line-Derived Neurotrophic Factor, Brain-Derived Neurotrophic Factor, and Cardiotrophin-1 with Tetanus Toxin
Authors: Rind Howard B. , Butowt Rafal , von Bartheld Christopher S.
Published: January 2005

Glial cell line-derived neurotrophic factor (GDNF), brain-derived neurotrophic factor (BDNF), and cardiotrophin-1 (CT-1) are the most potent neurotrophic factors for motoneurons, but their fate after retrograde axonal transport is not known. Internalized trophic factors may be degraded, or they may be recycled and transferred to other neurons, similar to the known route of tetanus toxin. We tested whether neonatal rat hypoglossal motoneurons target retrogradely transported trophic factors to synaptic sites on their dendrites within the brainstem and subsequently transfer these trophins across the synaptic cleft to afferent synapses (transsynaptic transcytosis). Motoneurons retrogradely transport from the tongue radiolabeled GDNF, BDNF, and CT-1 as well as tetanus toxin. Quantitative autoradiographic electron microscopy showed that GDNF and BDNF were transported into motoneuron dendrites with labeling densities similar to those of tetanus toxin. Although tetanus toxin accumulated rapidly (within 8 h) at presynaptic sites, GDNF accumulated at synapses more slowly (within 15 h), and CT-1 never associated with synapses. Thus, some retrogradely transported neurotrophic factors are trafficked similarly but not identically to tetanus toxin. Both GDNF and BDNF accumulate at the external (limiting) membrane of multivesicular bodies within proximal dendrites. We conclude that tetanus toxin, GDNF, and BDNF are released from postsynaptic sites and are internalized by afferent presynaptic terminals, thus demonstrating transsynaptic transcytosis. CT-1, however, follows a strict degradation pathway after retrograde transport to the soma. Synaptic and transcytotic trafficking thus are restricted to particular neurotrophic factors such as GDNF and BDNF.
Ein Modellgestützter Prädiktiver Ansatz zur Regelung von Ladedruck und AGR-Rate beim Nutzfahrzeug-Dieselmotor (A Model based Attempt to Control Boost Pressure and EGR-Rate for a Heavy Duty Engine)
Authors: Rückert Joachim , Richert Felix , Abel Dirk , Herrmann Olaf E. , Pfeifer Andreas , Schloßer Axel , Pischinger Stefan
Published: January 2005

Dieser Beitrag beschreibt die Entwicklung einer simultanen Regelung von Ladedruck und Abgasrückführrate für Nutzfahrzeug-Dieselmotoren [9]. Für die Regelung wird ein modellgestütztes prädiktives Verfahren eingesetzt. Im Rahmen des von der Europäischen Gemeinschaft geförderten Projektes “ATECS” (Advanced Truck Engine Control System) wurden als Entwicklungsumgebung nichtlineare Simulationsmodelle eines 12 Liter und eines 6 Liter Motors unter Matlab/Simulink® erstellt [7;13]. Diese Arbeiten wurden am Institut für Regelungstechnik (IRT) der RWTH Aachen in Zusammenarbeit mit dem Lehrstuhl für Verbrennungskraftmaschinen (VKA) der RWTH Aachen durchgeführt. Nach der Entwicklung und Erprobung in der Simulation wurde die Regelung in Zusammenarbeit mit dem VKA und der FEV Motorentechnik dort an einem 6 Liter Nutzfahrzeugmotor umgesetzt [4]. Die mit der Regelung erzielten transienten Emissionen wurden in zulassungsrelevanten Testzyklen ermittelt.
Stationäre und dynamische Motorvermessung zur Auslegung von Steuerkennfeldern – Eine kurze Übersicht (Static and Dynamic Measurements of Combustion Engines for Optimization of Control Mappings – A Brief Survey)
Authors: Zimmerschied Ralf , Weber Matthias , Isermann Rolf
Published: January 2005

In Form einer Übersicht werden unterschiedliche Vermessungsstrategien (Identifikationsmethoden) von Verbrennungsmotoren vorgestellt, die gegenüber den klassischen Rastermethoden eine wesentliche Verkürzung der Messzeit erzielen. Das Ziel der Vermessung ist die Modellbildung für die Offline-Optimierung von Steuerkennfeldern des stark nichtlinearen Systems Verbrennungsmotor mit mehreren Ein- und Ausgangsgrößen. Es werden stationäre und dynamische Vermessungs- sowie Modellbildungsmethoden vorgestellt.
Density of the System LiF–NaF–K2NbF7
Authors: Chrenková M. , Cibulková Jarmila , Šimko František , Daněk Vladimír
Published: January 2005

The density of the melts in the system LiF–NaF–K2NbF7 has been measured using an Archimedean method. Based on the measured density values, the molar volumes, partial molar volumes and excess molar volumes of the melts were calculated. The measurement of density in the investigated system has shown that a significant ternary interaction exists in the melts, which can be ascribed to the formation of different complex anions.
Achondroplasia
Authors: Pauli Richard M.
Published: January 2005

Achondroplasia is the most common of the skeletal dysplasias, arising in approximately 1 in 26,000 individuals. Most individuals with achondroplasia can be expected to have a normal life expectancy. However, they are at increased risk for a variety of medical sequelae, most of which are explicable on the basis of abnormalities of growth of cartilaginous bone or disproportionate growth of cartilaginous bone when compared with other contiguous tissues. Issues of concern include growth, motoric development, adaptive needs, hydrocephalus, cervicomedullary junction constriction, restrictive and obstructive pulmonary disease, middle ear dysfunction, kyphosis, lumbosacral spinal stenosis, bowing of the legs, and anesthetic risks. The natural history of achondroplasia can be beneficially modified by timely anticipatory medical care.
Fetal Anticonvulsant Syndrome
Authors: Gallagher Renata C. , Kingham Kerry , Hoyme H. Eugene
Published: January 2005

Fetal anticonvulsant syndrome refers to the increased birth prevalence of major malformations and the characteristic pattern of minor anomalies identified in some children born to women who have taken antiepileptic drugs during pregnancy. The major malformations described most frequently are those common in the general population: congenital heart defects, cleft lip and/or cleft palate, and genitourinary abnormalities. There is an even greater birth prevalence of major malformations in children born to women taking two antiepileptic drugs, and the prevalence of major malformations continues to increase with each additional antiepileptic drug taken during pregnancy. Microcephaly or growth retardation may be observed, particularly when there has been exposure to multiple antiepileptic drugs. A characteristic pattern of minor anomalies may be observed, including midface and digital hypoplasia, and there is an increased incidence of hemorrhagic disease of the newborn in children exposed to phenytoin, carbamazepine, and phenobarbital., We discuss the evaluation and management of children exposed to antiepileptic drugsin utero.
Gorlin Syndrome (Nevoid Basal Cell Carcinoma Syndrome)
Authors: Farndon Peter
Published: January 2005

Gorlin syndrome (nevoid basal cell carcinoma syndrome) is a multisystem disorder associated with mutations in the patched gene (PTCH). Two of the main features are recurrent odontogenic keratocysts and basal cell carcinomas. Thus, surveillance and long‐term support are of great clinical importance for people with Gorlin syndrome. The basal cell nevus that gives this condition its name is a unique type of basal cell carcinoma capable of aggressive behavior in adults. This condition is also associated with developmental anomalies, a recognizable facial appearance with macrocephaly and frontal bossing, ovarian fibroma, medulloblastoma, and cardiac fibroma. Some individuals have a particular sensitivity to therapeutic radiation. The prevalence of this autosomal dominant condition is said to be 1 in 40,000.
Klinefelter Syndrome
Authors: Simpson Joe Leigh , Graham John M. , Samango‐sprouse Carole , Swerdloff Ronald
Published: January 2005

In 1942, Klinefelter and colleagues delineated a syndrome in which postpubertal males showed normal external genitalia, gynecomastia and lack of pubertal virilization; small firm testes with tubular hyalinization with a decreased number of Leydig cells; azoospermia; elevated gonadotropin levels; and decreased 17‐ketosteroid levels. It was not until 1959 that the 47,XXY chromosome constitution was demonstrated. The incidence of Klinefelter syndrome is 1.2 per 1000 live‐born males. Minimal diagnostic criteria are now accepted to be the presence of at least one Y chromosome and two X chromosomes. Variants with three or four X chromosomes are less common. Klinefelter syndrome accounts for perhaps 5–15% of infertility in males, in particular, the group with oligospermia or azoospermia.
Myotonic Dystrophy Type 1
Authors: De Die‐smulders Christine E. M. , Jennekens Frans G. I. , Höweler Chris J.
Published: January 2005

Myotonic dystrophy type 1 is characterized by muscle weakness, myotonia, and multiple organ complications. Age of onset is very variable and is an important factor determining the clinical picture. The management is difficult due to the chronic course, the variability of symptoms, and the personality traits of myotonic dystrophy type 1 individuals. Annual follow‐up is recommended, using a standardized protocol such as the Cardiff Myotonic Dystrophy Muscle Clinic Record. Furthermore, education of affected individuals and their relatives and active dissemination of management protocols are important.
N
oonan Syndrome
Authors: Allanson Judith E.
Published: January 2005

Noonan syndrome is characterized by short stature, congenital heart defects, broad or webbed neck, unusual chest shape with superior pectus carinatum and inferior pectus excavatum, developmental delay of variable degree, cryptorchidism, and typical facies. Facial appearance changes considerably over time. Variable coagulation defects and lymphatic dysplasias are often found. It is a common autosomal dominant disorder that is frequently undiagnosed in the mildly affected individual. One gene responsible for Noonan syndrome,
PTPN11
, has been identified. The gene product SHP‐2 plays a role in development of the semilunar valves.
V
on
H
ippel–
L
indau Syndrome
Authors: Neil Schimke R. , Collins Debra L.
Published: January 2005

Von Hippel–Lindau syndrome is a multisystem disorder inherited as an incompletely penetrant autosomal dominant trait. The chief features of the syndrome are tumors, both benign and malignant. Multiple visceral cysts are common as well. The von Hippel–Lindau gene, located on chromosome 3p25‐26 is a recessive tumor‐suppressor gene. Its function is complex. Some genotype‐phenotype correlation exists. Effective treatment can be accomplished by early clinical and molecular identification of gene carriers. Anticipatory guidance is the key.
Multiple surface structures in polyolefins formed by modification methods
Authors: Nazarov V. G.
Published: January 2005

New methods for the formation of multiple surface structures in polyolefins were developed both at the molecular and macromolecular levels, which produced a high local nonuniformity of surface properties. In particular, I obtained varied molecular structures at the surface as a result of consecutive heterophase fluorination and sulfonation reactions of the polymers. Nonuniform macroscopic surface structures were formed with dosed thermal and deformation treatments of prefluorinated polymeric materials with the partial destruction of the formed modified layer and the subsequent predominant sulfonation of the disclosed macroscopic regions of the initial nonfluorinated polymer. The kinetics of the multiplet structure formation were studied. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 95:1198–1208, 2005
Structure and processability of iodinated poly(vinyl alcohol). II. Drawability of iodinated films
Authors: Shin Eun Joo , Lee Yang Hun , Choi Suk Chul
Published: January 2005

The drawability of poly(vinyl alcohol) (PVA) films iodinated with 0.1, 0.3, 0.5, 1.0, and 2.0 mol/L I2/KI aqueous solutions was examined with a tensile tester and a hand‐operated drawer at 30–150°C. The structure of the films drawn to a maximum draw ratio (MDR) and deiodinated was determined by X‐ray diffractometry, differential scanning calorimetry, and birefringence. Generally, the improvement of the drawability for the PVA film via iodination was ascertained by the increased breaking strain and decreased yield stress on the stress–strain curves when increasing the I2/KI concentration of the aqueous solutions used in the iodination. The MDR was generally increased with the concentration of I2/KI and the draw temperature. However, it diminished instead when close to the highest temperature and concentration of I2/KI, which was likely due to molecular degradation by the action of iodine as an oxidizer. The variation of the structure of the films drawn and deiodinated seems to be dependent mainly upon the MDR rather than the concentration of I2/KI. The greater the MDR was, the higher the degree of crystallinity, birefringence, and initial modulus were but the lower the melting temperature. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 95:1209–1214, 2005
Introduction to bioinformatics
Authors: Fenstermacher David
Published: January 2005

Bioinformatics 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

In 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

In 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

We 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

A 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

Bioinformatics 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

National 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

The 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

A 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

The 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

A 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

An 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

Sodium 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

A 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

Capillary 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

The 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”.
Trends in suicide by drowning in the elderly in England and Wales 1979–2001
Authors: Salib Emad
Published: January 2005

Background

Suicide by drowning increases with age but its rates vary between countries and among communities. Drowning suicide rates in some of the available studies may have been over reported or under reported because of misclassification.

Objective

This study presents data on the time trends, age/sex mortality rates from death by drowning in the elderly in England and Wales between 1979 and 2001. All coroners' verdicts in death by drowning; suicide, deaths undetermined whether accidentally or purposely inflicted were examined.

Methods

Counts of suicide due to drowning and submersion [ICD 9 codes; E954] and undetermined injury deaths [E984] (WHO, 1977), reported in England and Wales between 1979 and 2001 were obtained from National Statistics (ONS).

Results

There has been a gradual reduction in suicide by drowning in men and women by more than a third the observed count in 1979 (p < 0.01). However, this decline was less evident in the elderly particularly those over the age of 75. Elderly drownings appear to attract more verdicts of suicide compared to younger age groups (Odds Ratio 4.3 95% CI 2.3–8.3). Women, particularly elderly, are more likely to have a suicide verdict returned in drowning compared to men (Odds Ratio 1.5 95% CI 1.1–1.6).

Conclusions

The high rate of open verdicts in elderly drowning over the study period and compared to any other method of fatal self harm in England and Wales confirms the difficulties in reaching a firm conclusion in drowning death. Therefore combining suicide and all undetermined deaths in drowning as a matter of course, in nationally collected statistics, may result in grossly exaggerated rates and misleading trends in suicidal drowning. Suicide by drowning is probably not amenable to prevention and although the elderly are often thought to benefit more from suicide prevention than younger adults, the study findings seem to suggest that this is not likely to be the case in drowning. Copyright © 2005 John Wiley & Sons, Ltd.