bluuebunny/crossref_metadata_2025 huggingface dataset:
Gene selection and clustering for time-course
and dose–response microarray experiments using order-restricted inference
Authors: Peddada Shyamal D. , Lobenhofer Edward K. , Li Leping , Afshari Cynthia A. , Weinberg Clarice R. , Umbach David M.
Published: April 2003

We propose an algorithm for selecting and clustering genes according to their time-course or dose–response profiles using gene expression data. The proposed algorithm is based on the order-restricted inference methodology developed in statistics. We describe the methodology for time-course experiments although it is applicable to any ordered set of treatments. Candidate temporal profiles are defined in terms of inequalities among mean expression levels at the time points. The proposed algorithm selects genes when they meet a bootstrap-based criterion for statistical significance and assigns each selected gene to the best fitting candidate profile. We illustrate the methodology using data from a cDNA microarray experiment in which a breast cancer cell line was stimulated with estrogen for different time intervals. In this example, our method was able to identify several biologically interesting genes that previous analyses failed to reveal.

Contact: peddada@embryo.niehs.nih.gov

* To whom correspondence should be addressed.

† Present address: Amgen Inc. Thousand Oaks, CA 91320, USA.
GeneMerge—post-genomic analysis, data
mining, and hypothesis testing
Authors: Castillo-Davis Cristian I. , Hartl Daniel L.
Published: April 2003

Summary: GeneMerge is a web-based and standalone program written in PERL that returns a range of functional and genomic data for a given set of study genes and provides statistical rank scores for over-representation of particular functions or categories in the data set. Functional or categorical data of all kinds can be analyzed with GeneMerge, facilitating regulatory and metabolic pathway analysis, tests of population genetic hypotheses, cross-experiment comparisons, and tests of chromosomal clustering, among others. GeneMerge can perform analyses on a wide variety of genomic data quickly and easily and facilitates both data mining and hypothesis testing.

Availability: GeneMerge is available free of charge for academic use over the web and for download from: http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html.

Contact: ccastillo-davis@oeb.harvard.edu

Supplementary information: http://www.oeb.harvard.edu/hartl/lab/publications/GeneMerge.html

* To whom correspondence should be addressed.
EVOLUTIONARY OPTIMIZATION OF GAUSSIAN WINDOWING FUNCTIONS FOR DATA PREPROCESSING
Authors: COURTE DALE E. , RIZKI MATEEN M. , TAMBURINO LOUIS A. , GUTIERREZ-OSUNA RICARDO
Published: April 2003

The average classification accuracy of an odor classification system is improved using a genetic algorithm to determine optimal parameters for feature extraction. Gaussian windowing functions, called "kernels" are evolved to extract information from the transient response of an array of gas sensors, resulting in a reduced set of extracted features for a linear discriminant pattern classification system. Results show significant improvements are achieved when compared to results obtained using a predetermined and fixed set of four bell-shaped kernels for every sensor. Examination of the evolved kernels reveals the areas of the sensor responses where discriminating information was identified. A novel data migration approach during training helps prevent overtraining, and the fitness measure chosen incorporates adjustments for both population diversity and solution complexity. A variety of adjustable parameters, including the definition of a time-varying dynamic weighting factor, encourage experimentation in order to appropriately tune the sampling methods and fitness measure.
A SYNERGISTIC MODEL FOR REPRESENTING AND INTERPRETING HUMAN ACTIVITIES AND EVENTS FROM VIDEO
Authors: BOURBAKIS NIKOLAOS , GATTIKER JIM R. , BEBIS GEORGE
Published: April 2003

This paper describes a new and innovative and approach for representing, recognizing and interpreting human activity from video, contributing to an automated system capable of recognition of complex human behaviors. This technology is directly applicable for monitoring public safety and law enforcement, and capturing of activities is crucial for supporting virtual collaborations between citizens, and between citizens and government. Digital video stores of terabytes are now common, and will continue to increase until they dominate stored data. The government of the future will have to manage, organize, recall, and interpret information from this resource, This paper addresses one important facet of this.

The approach presented here is a model based on the hierarchical synergy of three other models: the Local/Global (L-G) graph, the Stochastic Petri Net (SPN) graph and a neural network (NN) model. The application focus is the description of activity of actors in a video (or multi-sensor) scene, from the snapshot state description through higher levels of organization into events. The concept of importance is the distinction and interaction between structural knowledge, or knowledge about physical state, and functional knowledge, knowledge about change and events. The L-G graph provides a powerful description of the structural image features presented in an event, and the SPN model offers a description of the functional behavior. The NN (or other adaptive) model provides the capability of leaning behavioral patterns for classification of posture and activity, and forecasting possible events in a free environment.
Expert testimony in court. 1: General principles
Authors: Casey Patricia
Published: April 2003

Since the Woolf reforms were incorporated into legal practice in civil cases in England and Scotland, there has been a distinction between expert and professional witnesses. A common feature is the appointment of an agreed expert to give evidence on aspects of a case that require expert testimony. These changes do not apply in criminal cases nor in other jurisdictions such as the Republic of Ireland. However, all witnesses, whether professional or expert, must be objective, since their role is to assist the court. There is little or no training of clinicians in how to become an expert and suggestions for improving this are discussed. Practical aspects of accepting a brief from a solicitor are considered.
Magnetically Induced Large Mesoporous Single‐Domain Monoliths Using a Mineral Liquid Crystal as a Template
Authors: Camerel F. , Gabriel J.‐C.P. , Batail P.
Published: April 2003

In this paper, we report on how the properties of the suspensions of a lyotropic nematic mineral liquid crystal (MLC) based on V2O5 ribbons are exploited to synthesize single‐domain mesostructured inorganic–inorganic composites, aligned at the centimeter length scale by application of a relatively small magnetic field (0.85 T). In addition, the removal of the mineral template from the inorganic matrix leaves aligned empty channels, fingerprints of the V2O5 ribbons. Large colorless and birefringent mesoporous material is obtained where the orientational order of the channel director has retain the magnetic‐field alignment of its mineral template up to the centimeter length scale within the porous macroscopic silica matrix. A representative material exhibits slit‐like pores with cross‐sectional dimensions of 2 × 20 nm over 600 nm, and has a specific surface area of 207 m2 g–1.
Social and familial context of prenatal genetic testing decisions: Are there racial/ethnic differences?
Authors: Learman Lee A. , Kuppermann Miriam , Gates Elena , Nease Robert F. , Gildengorin Virginia , Washington A. Eugene
Published: April 2003

The purpose of this cross‐sectional study of 999 socioeconomically and racially/ethnically diverse pregnant women was to explore prenatal genetic testing attitudes and beliefs and the role of external influences. Surveys in English, Spanish, and Chinese included questions regarding the value of testing, pregnancy, and motherhood; the acceptability of Down syndrome in the subject's community; and the role of social and cultural influences in prenatal testing decisions. We analyzed racial/ethnic differences in all attitudinal and external influence variables, controlling for age, relationship status, and socioeconomic status. We found statistically significant racial/ethnic group differences in familiarity with an individual with Down syndrome and in 10 of 12 attitude, belief, and external influence variables, even after controlling for other sociodemographic characteristics. We also observed substantial variation within racial/ethnic groups for each of these measures. Despite the statistically significant group differences observed, R2 values for all multivariate models were modest and response distributions overlapped substantially. Social and familial contexts for prenatal testing decisions differ among racial/ethnic groups even after accounting for age, marital status, and other socioeconomic factors. However, substantial variation within groups and overlap between groups suggest that racial/ethnic differences play a small role in the social and familial context of prenatal genetic testing decisions. © 2002 Wiley‐Liss, Inc.
Effect of family history on disclosure patterns of cystic fibrosis carrier status
Authors: Ormond Kelly E. , Mills Patti L. , Lester Lucille A. , Ross Lainie F.
Published: April 2003

As general population screening becomes more common, an increasing number of cystic fibrosis (CF) carriers will be identified who do not have a family history of CF. Whether these carriers inform their relatives of their carrier status and whether their relatives are motivated to pursue carrier screening is unknown. We surveyed CF carriers with and without a family history of CF to understand whether and how information dissemination patterns differ, why information is or is not shared, and to what extent relatives are known to undergo testing. CF carriers were identified from a general population carrier screening clinic (group B = 18) or were parents of affected children followed at a CF clinic (group A = 30). CF carriers with a family history told essentially 100% of their living parents, siblings, and half‐siblings, while those without a family history told 84% of living parents and 56% of siblings (P < 0.05). Despite the high rate of information dissemination in both groups, few siblings were known to have undergone carrier screening (14/74). Significantly fewer second‐ and third‐degree relatives were informed about carrier status or were known to have undergone carrier screening. Group A was more likely to inform second‐ and third‐degree relatives about carrier status. Our study documents that the frequency and reasons for disclosing CF carrier status differ between individuals with and without a family history of CF despite the fact that the reproductive risks for their relatives are the same. © 2003 Wiley‐Liss, Inc.
Jüngste Entwicklungen bei der gekreuzten Olefinmetathese
Authors: Connon Stephen J. , Blechert Siegfried
Published: April 2003

Unter den vielen übergangsmetallvermittelten C‐C‐verknüpfenden Reaktionen ist die Olefinmetathese in den letzten Jahren durch die große Bandbreite an möglichen Umsetzungen mit käuflichen und leicht handhabbaren Katalysatoren hervorgetreten und gilt heutzutage als eine der mächtigsten Synthesemethoden in der Organischen Chemie. Die intermolekulare Variante dieser Reaktion, die Kreuzmetathese, führte trotz ihres hohen synthetischen Nutzens bis vor kurzem eher ein Schattendasein. Durch die Entwicklung neuer, besserer Katalysatoren konnte die Selektivität, die Toleranz gegen funktionelle Gruppen und die Effizienz der Katalyse jedoch auf ein Niveau gesteigert werden, das noch bis vor wenigen Jahren als unvorstellbar galt. Dank dieser Fortschritte und dem verbesserten Verständnis des Reaktionsmechanismus und der Katalysator‐Substrat‐Wechselwirkungen werden Kreuzmetathesen heute in zunehmendem Maße in mehrstufigen Reaktionssequenzen und Naturstoffsynthesen verwendet. Die kürzlich vorgestellte Einbeziehung von Alkinen und sterisch gehinderten bicyclischen Olefinen als Substrate für bimolekulare Kupplungen, die Entwicklung von enantioselektiven und in Wasser ausführbaren Kreuzmetathesen und die erfolgreiche Kombination der Olefinmetathese und der Festphasensynthese in der Organischen Chemie haben die Anwendungsbreite der Kreuzmetathese noch zusätzlich vergrößert.
Recent Developments in Olefin Cross‐Metathesis
Authors: Connon Stephen J. , Blechert Siegfried
Published: April 2003

Among the many types of transition‐metal‐catalyzed CC bond‐forming reactions, olefin metathesis has come to the fore in recent years owing to the wide range of transformations that are possible with commercially available and easily handled catalysts. Consequently, olefin metathesis is now widely considered as one of the most powerful synthetic tools in organic chemistry. Until recently the intermolecular variant of this reaction, cross‐metathesis, had been neglected despite its potential. With the evolution of new catalysts, the selectivity, efficiency, and functional‐group compatibility of this reaction have improved to a level that was unimaginable just a few years ago. These advances, together with a better understanding of the mechanism and catalyst–substrate interactions, have brought us to a stage where more and more researchers are employing cross‐metathesis reactions in multistep procedures and in the synthesis of natural products. The recent inclusion of alkynes and hindered bicyclic olefins as viable substrates for bimolecular metathesis coupling, the discovery of enantioselective cross‐metathesis and cross‐metathesis in water, and the successful marriage of metathesis and solid‐phase organic synthesis has further widened the scope of this versatile reaction.
The loss of genetic diversity in Dabry's sturgeon (Acipenser dabryanus, Dumeril) as revealed by DNA fingerprinting
Authors: Wan Qiu‐Hong , Fang Sheng‐Guo , Li Ya‐Nan
Published: April 2003

Dabry's sturgeon, a large, long‐lived migratory fish is endemic to the Yangtze River. Over‐fishing and habitat destruction have caused large‐scale declines in natural stocks in the last two decades.

Examining patterns of genetic diversity has become an integral component of many management plans for endangered species. DNA fingerprinting was applied to detect genetic diversity in Dabry's sturgeon collected in 1958–1959, 1980–1981 and 1998–1999.

Studies on direct genetic parameters (genetic variability, hypervariable loci and heterozygosity) and indirect parameters (band‐sharing coefficient and allelic frequency) showed that the continuous decline in wild populations has caused the loss of genetic diversity in present‐day sturgeon.

The present‐day populations have the lowest genetic variability; thus, effective management is needed to preserve genetic diversity.

A conservation strategy is urgently required, comprising artificial rearing facilities coupled with breeding management plans.

Copyright © 2003 John Wiley & Sons, Ltd.
Ontologies: Formalising biological knowledge for bioinformatics
Authors: Bard Jonathan
Published: April 2003

An ontology is a domain of knowledge structured through formal rules so that it can be interpreted and used by computers. Ontologies are becoming increasingly important in bioinformatics because they can be linked to the information in databases and their knowledge then used to query the databases. Typical examples in current use are the Gene Ontology, which incorporates much of our knowledge about gene products, and ontologies of developmental anatomy, which, for example, facilitate tissue‐based queries to gene expression databases both textually and spatially. This article considers the production, formulation and types of bio‐ontologies together with the reasons why they are so useful. © BioEssays 25:501–506, 2003. © 2003 Wiley Periodicals, Inc.
Teratogenic alleles and neurodevelopmental disorders
Authors: Johnson William G.
Published: April 2003

The genetic interaction between mother and fetus during pregnancy is discussed, focusing on teratogenic alleles that act in the mother to alter fetal development and contribute to a neurodevelopmental disorder. For these alleles, the mother is the genetic patient. Teratogenic alleles interact with modifying and specificity alleles that act in the fetus and with environmental factors. Based on examples of the model, two candidate mechanisms emerge as contributors to neurodevelopmental disorders, folate‐homocysteine pathways and immune/inflammatory mechanisms. Both, acting in mothers, affect fetal development and contain many polymorphic genes. These two systems interact with each other. Common functional polymorphisms of mild effect in these two systems of interacting genes are good candidates for teratogenic alleles. The presence of teratogenic alleles complicates gene identification for neurodevelopmental disorders. However, using the special methods required to identify teratogenic alleles is important because this could lead to new approaches to prevention and improved therapy of these disorders. BioEssays 25:464–477, 2003. © 2003 Wiley Periodicals, Inc.
Pathfinding and growth termination of primary trigeminal sensory afferents in the embryonic rat hindbrain
Authors: Miyahara Mikiko , Shirasaki Ryuichi , Tashiro Yasura , Muguruma Keiko , Heizmann Claus W. , Murakami Fujio
Published: April 2003

Axons of the trigeminal ganglion convey sensory information from mechanoreceptors, thermoreceptors, and nociceptors in the face and nasal mucosa, then terminate on several groups of neurons including the principal sensory nucleus and the nuclei of the spinal trigeminal tract. To understand guidance mechanisms during the development of trigeminal sensory axons (TA) in the embryonic brain, we first investigated the growth pattern of TA in relation to organization in the hindbrain using flat whole‐mount preparation from rat. We found that the primary TA from the trigeminal ganglion entered the brainstem and grew longitudinally within the hindbrain. Whereas descending axons ran just medial to the primary vestibular axons to innervate the spinal nucleus, ascending axons stayed near the entry point. In flat whole‐mount culture, the TA extended both ascending and descending branches as they do in vivo. Rostral hindbrain was found to be a less permissive substrate for the TA compared to caudal hindbrain. In addition, the nonpermissive property of the ventral hindbrain substrate restricted the invasion of TA along the entire length of the hindbrain. Thus, cooperation of absolute and relative permissiveness of the substrate plays important roles in the guidance of TA to their targets. J. Comp. Neurol. 460:503–513, 2003. © 2003 Wiley‐Liss, Inc.
CD2 mediates activation of the IFN‐γ intronic STAT binding region in mucosal T cells
Authors: Gonsky Rivkah , Deem Richard L. , Young Howard A. , Targan Stephan R.
Published: April 2003

The pathways leading to activation of mucosal lamina propria (LP) T cells differ from those of peripheral T cells. LP T cells exhibit enhanced IFN‐γ secretion when activated through the CD2 pathway. This study demonstrates CD2 signaling is followed by activation of STAT proteins in both peripheral blood mononuclear cells (PBMC) and lamina propria mononuclear cells (LPMC), although, distinct differences exist in regulation of IFN‐γ promoter gene expression. Both PBMC and LPMC exhibit enhanced secretion and transactivation of the –2.7 kb IFN‐γ promoter region following CD2 signaling, but the IFN‐γ STAT‐binding region (within the first intron) serves as an orientation‐independent enhancer of promoter activity only in LPMC. Mutation of the STAT site impairs enhancer activity. In LPMC, but not PBMC, CD2 mediates binding of STAT1 and STAT4 to the IFN‐γ intronic element. Unstimulated LMPC exhibit low levels of phosphotyrosine‐STAT4 and STAT1 and phosphoserine‐STAT1, which increase substantially following CD2 activation. In PBMC, CD2‐mediated phosphorylation is primarily restricted to enhanced levels of phosphotyrosine‐STAT1. Thus, these results indicate that both common as well as unique molecular mechanisms are involved in CD2 signaling and activation of the STAT pathway in LP T cells which are critical for regulation of IFN‐γ expression in the gut.
TNF‐α impairs peripheral tolerance towards β‐cells, and local costimulation by B7.1 enhances the effector function of diabetogenic T cells
Authors: Skak Kresten , Guerder Sylvie , Picarella Dominic E. , Brenden Nina , Flavell Richard A. , Michelsen Birgitte K.
Published: April 2003

Maintenance of peripheral tolerance and inactivation of autoreactive T cells is based on a delicate balance between pro‐inflammatory and protective cytokines that is poorly understood. We havehere addressed how the local expression of the inflammatory cytokine TNF‐α can impair peripheral tolerance and lead to autoreactivity. After transplantation of pancreata that are immunogenic due to β‐cell expression of B7.1 and TNF‐α, into thymectomized and euthymic syngeneic mice, we found that only euthymic mice rejected the grafts. This result suggests that under normal circumstances autoreactive T cells are functionally inactivated, and initiation of an autoreactive response requires de‐novo generation of T cells. By contrast, thymectomized mice expressing TNF‐α on the endogenous islets rejected the grafts, showing that expression of TNF‐α prevents functional silencing of the autoreactive T cells. Thus, this study provides a mechanism by which TNF‐α and possibly chronic inflammatory responses may promote autoimmune diseases. Furthermore, we have investigated whether B7.1 can enhance T cell responses of already activated T cells leading to islet rejection. By transplantation of wild‐type and B7.1‐expressing islets into overtly diabetic mice we found that only the wild‐type islets could restore normoglycemia, suggesting that costimulation by B7.1 is required in the expansion or effector phase of the response.
Decreasing the threshold for thymocyte activation biases CD4+ T cells toward a regulatory (CD4+CD25+) lineage
Authors: Stephens Geoffrey L. , Ignatowicz Leszek
Published: April 2003

Thymus‐derived CD4+CD25+ regulatory T (Tr) cells play a critical role in suppressing aberrant responses to self in vivo. The factors that influence a CD4+ T cell's decision to commit to an immunoregulatory Tr cell lineage are currently unknown. In the present study, we found that in mice, abundantly expressing a few or one peptide(s) bound to MHC class II molecules, a large portion of conventional CD4+ T cells could be biased towards the commitment to a Tr lineage by reducing the threshold required for thymocyte activation. This occurred in the presence of either an antisense glucocorticoid receptor transgene or a pharmacological inhibitor of glucocorticoid synthesis. These results demonstrate a novel in vivo pathway for the generation of Tr cells, and raise the possibility that therapeutic enhancement of the Tr cell repertoire through pharmacological manipulation of TCR signaling thresholds may provide a feasible means of ameliorating autoimmunity.
Exchange Interactions and Covalency in Dinuclear Complexes of Iron(III) and Gallium(III) Containing the Redox‐Noninnocent Ligand 1,2‐Bis(3,5‐di‐tert‐butyl‐2‐hydroxyphenyl)oxamide
Authors: Beckmann Udo , Bill Eckhard , Weyhermüller Thomas , Wieghardt Karl
Published: April 2003

The dinucleating ligand 1,2‐bis(3,5‐di‐tert‐butyl‐2‐hydroxyphenyl)oxamide [H4(bbpo)] has been synthesized. From its reaction with GaCl3 or FeCl3 in CH3OH/NaOH the salts [N(nBu)4]2[MIII2(bbpo)Cl4] [M = Ga (1), Fe (2)] have been isolated as crystalline solids upon addition of [N(nBu)4]Cl. Complexes 1 and 2 have been characterized by single‐crystal X‐ray crystallography. Cyclic voltammetry established that both species undergo two successive, reversible one‐electron oxidations in CH2Cl2 {0.10 M [N(nBu)4]PF6} which are shown to be ligand‐centered: one and then two N,O‐coordinated o‐iminobenzosemiquinonate π‐radicals form which couple antiferromagnetically with the high‐spin ferric ions in 2. Thus, the monoanion of 2 has an St = 1/2 ground state. The complexes have been characterized by Mössbauer, UV/Vis, and EPR spectroscopy. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Mechanisms of the Axial Ligand Substitution Reactions of Dinuclear, Head‐to‐Head α‐Pyrrolidonato‐ and Pivalamidato‐Bridged cis‐Diammineplatinum(III) Complexes with Halide Ions
Authors: Shimazaki Kazuhiro , Sekiya Hideo , Inoue Haruhiko , Saeki Nami , Ishihara Koji , Matsumoto Kazuko
Published: April 2003

The acid dissociation constant of the axial aqua ligand in the Head‐to‐Head (HH) dinuclear pivalamidato‐bridged cis‐diammineplatinum(III) complex ([(H2O)Pt(NH3)2(μ‐C5H10NO)2Pt(NH3)2(H2O)]4+) and the formation constants of the successive substitution reactions on the axial sites of the HH α‐pyrrolidonato‐bridged cis‐diammineplatinum(III) dinuclear complex and the HH pivalamidato‐bridged cis‐diammineplatinum(III) dinuclear complex with halide ions X− (X− = Cl− and Br−) to give monohalo and dihalo complexes were determined spectrophotometrically at 25 °C and I = 2.0 M. A kinetic study was also performed for the monohalo and dihalo complex formations. The effect of the bridging ligand upon the axial site reactivity was compared and discussed. The ligand substitution behavior of the monohalo complex was affected by the axial ligand on the opposite Pt site and also by the bridging ligand. For both the α‐pyrrolidonato‐ and the pivalamidato‐bridged complexes, the formation of dichloro complexes proceeds only through the simple substitution path (k2 path), whereas the formation of dibromo complexes proceeds through the two parallel reaction paths: the k2 and k3 paths for the former and the k2 and k2# paths for the latter. The difference of the reaction paths is reasonably explained by the different trans effect of the halide ion on the opposite axial site for the former complex, but for the latter complex, the reaction paths are not easy to explain. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
A New Concept for the Efficient Synthesis of Chiral Phosphorus−Nitrogen−Carbon Cage Compounds
Authors: Hoffmann Nils , Wismach Catleen , Ernst Ludger , Schiebel Hans‐Martin , Jones Peter G. , Streubel Rainer
Published: April 2003

A new concept for the efficient synthesis of a chiral phosphorus‐nitrogen‐carbon cage‐compound is reported, which is comprised of a high‐yield three‐step procedure starting from a P‐Cp*‐substituted 2H‐azaphosphirene complex. Thermolysis of a solution of the latter complex in the presence of Ph3PNCN and DMAD afforded the P‐Cp*‐substituted 2H‐1,2‐azaphosphole complex 11 in a clean reaction; a further reaction at 75 °C with DMAD produced complex 12 via an intermolecular Diels−Alder reaction of the Cp* group. A subsequent intramolecular Diels−Alder reaction of 12, at 120 °C, yielded the title compound, complex 13, in quantitative yields. Elemental analyses and detailed (solution) NMR spectroscopic and MS investigations confirmed all complexes. Furthermore, solid state structures of complexes 11 and 13 were established by X‐ray single crystal structure analyses. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003)
Cover Picture: Solvothermal Synthesis of a Layered Open‐Framework Chlorocadmium Oxalate, Cd2(C2O4)0.5Cl3NaCl·4H2O (Eur. J. Inorg. Chem. 9/2003)
Authors: Vaidhyanathan R. , Natarajan Srinivasan , Rao C. N. R.
Published: April 2003

The cover picture shows a schematic illustration of the unusual inorganic‐organic hybrid structures (upper right) formed by linking of the inorganic building units through organic linkers. The structures of two different compounds (bottom) containing the inorganic cadmium chloride chains (upper left corner) linked by oxalate and piperazine moieties into two and three dimensions are also shown. Color scheme: Cd − yellow; Cl − green; O − red; N − violet; C − blue. Details are discussed in the article by C. N. R. Rao et al. on p. 1675 ff.
Binding Curve from Normalized Limiting Currents of Labile Heterogeneous Metal‐Macromolecular Systems. The Case of Cd/Humic Acid
Authors: Companys Encarnació , Puy Jaume , Torrent Marià , Galceran Josep , Salvador José , Garcés Josep Lluís , Mas Francesc
Published: April 2003

A set of titrations of different amounts of humic acid with cadmium are performed at pH 6.0 and fixed ionic strength (0.1 M KNO3). Both reverse pulse polarograms, which minimize the electrodic adsorption effects on the limiting current, and potentiometric measurements with an ion selective electrode are recorded along the titrations. The free metal concentration is determined from the polarographic measurement by means of an iterative numerical method recently developed. The resulting binding curve is found to agree very well with the one obtained through the potentiometric data obtained along the same titration. After application of the Donnan model to correct for polyelectrolytic effects, different complexation isotherms have been used to fit the specific binding. Complexation parameters for the Cd/HA system obtained with a Langmuir‐Freundlich and Gaussian isotherms are briefly discussed.
Development of a Multiresidue Liquid Chromatography Method with Electrochemical Detection (HPLC‐ECD) for the Determination of Macrolide Antibiotics
Authors: González de la Huebra María José , Bordin Guy , Rodríguez Adela Rosa
Published: April 2003

A multiresidue high performance liquid chromatography procedure with electrochemical detection (amperometric) (HPLC‐ECD) using a C18 narrow bore column was fully optimized for the separation of a standard mixture of macrolides. Up to five macrolides, josamycin (JOS), kitasamycin (KIT), rosamicin (ROS) roxithromycin (ROX) and oleandomycin (OLE), the latter being selected as internal standard for the quantification, were properly separated using an isocratic elution mode. The influence of classical chromatographic and instrumental parameters was investigated in order to optimize them before the calibration assay. The method was succesfully applied to the determination of ROS and ROX in human urine.
Bioelectrocatalytical Detection of H2O2 with Different Forms of Horseradish Peroxidase Directly Adsorbed at Polycrystalline Silver and Gold
Authors: Ferapontova Elena , Gorton Lo
Published: April 2003

The bioelectrocatalytical reduction of H2O2 based on direct electron transfer (ET) between polycrystalline silver and the heme containing active site of horseradish peroxidase (HRP) is studied and compared with that obtained at gold. Native HRP and recombinant wild type HRP, containing additionally a six‐histidine tag at the N‐terminus, NHisrHRP, have been used for adsorptive modification of the electrodes. The histidine sequences, introduced into the peroxidase structure by genetic engineering of recombinant HRP using an E. coli expression system, were supposed to affect adsorption/orientation of the enzyme at the electrode surface. The variations in direct ET efficiency when changing from gold to silver, as well as from native HRP to NHisrHRP are analyzed and discussed, specifically, the high ET rates obtained with NHisrHRP‐modified preoxidized gold and silver electrodes, though accompanied by extremely rapid loss of the biolectrocatalytical activity of the latter (silver) in direct (but not mediated) ET. The advantages and drawbacks of the studied HRP‐electrode systems for the electroanalytical detection of H2O2 are considered.
Ceramic Carbon Electrode Modified with Butyloferrocene
Authors: Saczek‐Maj Monika , Opallo Marcin
Published: April 2003

Ceramic carbon electrode modified with butyloferrocene was prepared and studied. The electrode consists of graphite powder, homogeneously dispersed in hydrophobic silica matrix. The latter was obtained from organically modified silicate – methyltrimethoxysilane by sol‐gel process. After gelation and drying it was filled with redox liquid – butyloferrocene by immersion. The properties of the electrode were investigated by cyclic voltammetry and chronoamperometry in aqueous salt solution of different concentration. The cyclic polarization of the electrode in aqueous electrolyte results in peak shaped voltammogram, stable during continuous potential cycling. The modification of the electrode with butyloferrocene diluted by hydrophobic non‐electroactive solvent like hexadecane leads to a decrease of the current. The specific voltammogram features were attributed to the redox process of butyloferrocene. The magnitude of the current is proportional to the aqueous electrolyte concentration. It has been concluded that the electrooxidation of redox liquid within hydrophobic silicate matrix is followed by anion transfer from aqueous phase. The electrode process occurs at the three phase junction formed by graphite particles and liquid organic‐aqueous interface supported by hydrophobic silicate.
Electrophoresis of biological cells: Charge‐regulation and multivalent counterions association model
Authors: Hsu Jyh‐Ping , Hsieh Tien‐Shiang , Young Tai‐Horng , Tseng Shiojenn
Published: April 2003

The electrophoresis of a biological cell is analyzed theoretically. An entity, which is of amphoteric nature, is used to simulate its electrophoretic behavior. To reflect conditions of practical interest, we assume that the liquid phase contains mixed (a:b)+(c:b) electrolytes, where a and c are the valences of cations, and b is the valence of anions. We consider the case where the surface of a cell contains both bivalent acidic and monovalent basic functional groups, the dissociation/association of them yields fixed surface charge, and the multivalent cations in the liquid phase are allowed to combine with dissociated acidic functional groups, which has the effect of lowering the charge density on cell surface. The electrophoretic behaviors of a cell under various conditions are illustrated. The results obtained can be used to identify the types of functional groups that may be present on cell surface. On the other hand, if the surface functional groups involved in cell electrophoresis are known, then their density and the associated dissociation/association constants can be estimated from experimental data.
Direct and specific recognition of glycosaminoglycans by antibodies after their separation by agarose gel electrophoresis and blotting on cetylpyridinium chloride‐treated nitrocellulose membranes
Authors: Maccari Francesca , Volpi Nicola
Published: April 2003

A method for the immunodetection of several natural complex polysaccharides (glycosaminoglycans) after their separation by conventional agarose gel electrophoresis, blotting and immobilizing on nitrocellulose membranes derivatized with the cationic detergent cetylpyridinium chloride (CPC), and direct and specific immunodetection by antibodies is described. This new approach is based on the principles that were used to develop the Western blot, and is applied to the separation of the glycosaminoglycans purified from normal human urine. After migration in agarose gel electrophoresis, chondroitin sulfate samples of different origin were blotted and transferred onto nitrocellulose membranes treated with CPC. Immunodetection was performed using the anti‐chondroitin‐6‐sulfate antibody that specifically recognizes intact chondroitin‐6‐sulfate. By calculating the ratio between the antibody staining (epitope) and alcian blue staining (mass), the epitope density expressed as a percentage, i.e., the number of repetitive epitopes per mass, was obtained. These values were in agreement with the quantitation of 6‐sulfated groups of chondroitin sulfate performed by the evaluation of unsatured disaccharide‐6‐sulfate (ΔDi6S) produced after treatment with chondroitinase ABC and separated by high‐performance liquid chromatography (HPLC). Furthermore, immunodetection of heparan sulfate was performed using the anti‐heparan sulfate antibody.
Chiral resolution of some environmental pollutants by capillary electrophoresis
Authors: Ali Imran , Gupta Vinod K. , Aboul‐Enein Hassan Y.
Published: April 2003

The chiral resolution of the environmental pollutants by capillary electrophoresis is reviewed. Various aspects of the chiral resolution such as chiral selectors, optimization of capillary electrophoresis conditions including composition of the background electrolyte (BGE), pH of the BGE, ionic strength of the BGE, structures and types of the chiral selectors, applied voltage, temperature, structures of the chiral pollutants, use of organic modifiers and other parameters are presented. Furthermore, detection, sample treatment, validation of the methods, and the chiral recognition mechanisms, have been discussed.
Comprehensive two‐dimensional separations based on capillary high‐performance liquid chromatography and microchip electrophoresis
Authors: Yang Xiuhan , Zhang Xiangmin , Li Aizhen , Zhu Shiyang , Huang Yiping
Published: April 2003

A novel comprehensive two‐dimensional (2‐D) separation system coupling capillary high‐performance liquid chromatography (cHPLC) with microchip electrophoresis (chip CE) is demonstrated. Reversed‐phase cHPLC was used as the first dimension, and chip CE acted as the second dimension to perform fast sample transfers and separations. A valve‐free gating interface was devised simply by inserting the outlet‐end of LC column into the cross‐channel on a specially designed chip. A home‐made confocal laser‐induced fluorescence detector was used to perform on‐chip high‐sensitive detection. The cHPLC effluents were continuously delivered to the chip and pinched injections of the effluents every 20 seconds were employed for chip CE separation. Gradient elution of cHPLC was carried out to obtain the high‐efficiency separation. Free‐zone electrophoresis was performed with triethylamine buffer to achieve high‐speed separation and prevent sample adsorption. Such a simple‐made comprehensive system was proved to be effective. The relative standard deviations for migration time and peak height of rhodamine B in 150 sample transfers were 3.2% and 9.8%, respectively. Peptides of the fluorescein isothiocyanate (FITC)‐labeled tryptic digests of bovine serum albumin were fairly resolved and detected with this comprehensive 2‐D system.
Estimation of fundamental periods of shear‐wall dominant building structures
Authors: Balkaya Can , Kalkan Erol
Published: April 2003

Shear‐wall dominant multistorey reinforced concrete structures, constructed by using a special tunnel form technique are commonly built in countries facing a substantial seismic risk, such as Chile, Japan, Italy and Turkey. In spite of their high resistance to earthquake excitations, current seismic code provisions including the Uniform Building Code (International Conference of Building Officials, Whittier, CA, 1997) and the Turkish Seismic Code (Specification for Structures to be Built in Disaster Areas, Ankara, Turkey, 1998) present limited information for their design criteria. In this study, consistency of equations in those seismic codes related to their dynamic properties are investigated and it is observed that the given empirical equations for prediction of fundamental periods of this specific type of structures yield inaccurate results. For that reason, a total of 80 different building configurations were analysed by using three‐dimensional finite‐element modelling and a set of new empirical equations was proposed. The results of the analyses demonstrate that given formulas including new parameters provide accurate predictions for the broad range of different architectural configurations, roof heights and shear‐wall distributions, and may be used as an efficient tool for the implicit design of these structures. Copyright © 2003 John Wiley & Sons, Ltd.
System identification of instrumented bridge systems
Authors: Arici Yalin , Mosalam Khalid M.
Published: April 2003

Several recorded motions for seven bridge systems in California during recent earthquakes were analysed using parametric and non‐parametric system identification (SI) methods. The bridges were selected considering the availability of an adequate array of accelerometers and accounting for different structural systems, materials, geometry and soil types. The results of the application of SI methods included identification of modal frequencies and damping ratios. Excellent fits of the recorded motion in the time domain were obtained using parametric methods. The multi‐input/single‐output SI method was a suitable approach considering the instrumentation layout for these bridges. Use of the constructed linear filters for prediction purposes was also demonstrated for three bridge systems. Reasonable prediction results were obtained considering the various limitations of the procedure. Finally, the study was concluded by identifying the change of the modal frequencies and damping of a particular bridge system in time using recursive filters. Copyright © 2003 John Wiley & Sons, Ltd.
Dynamic stiffness of foundation embedded in layered halfspace based on wave propagation in cones
Authors: Wolf John P. , Preisig Matthias
Published: April 2003

An Erratum has been published for this article in Earthquake Engineering & Structural Dynamics 33(6) 2004, 793.The dynamic stiffness of a foundation embedded in a multiple‐layered halfspace is calculated postulating one‐dimensional wave propagation in cone segments. In this strength‐of‐materials approach the sectional property of the cone segment increases in the direction of wave propagation. Reflections and refractions with waves propagating in corresponding cone segments occur at layer interfaces. Compared to rigorous procedures the novel method based on cone segments is easy to apply, provides conceptual clarity and physical insight in the wave propagation mechanisms.

This method postulating one‐dimensional wave propagation in cone segments with reflections and refractions at layer interfaces is evaluated, calculating the dynamic stiffness of a foundation embedded in a multiple‐layered halfspace. For sites resting on a flexible halfspace and fixed at the base, engineering accuracy (deviation of ±20%) is achieved for all degrees of freedom with a vast parameter variation. The behaviour below the cut‐off frequency in an undamped site fixed at its base is also reliably predicted. The accuracy is, in general, better than for the method based on cone frustums, which can lead to negative damping. Copyright © 2003 John Wiley & Sons, Ltd.
Application of non‐linear multiple tuned mass dampers to suppress man‐induced vibrations of a pedestrian bridge
Authors: Poovarodom Nakhorn , Kanchanosot Sopak , Warnitchai Pennung
Published: April 2003

This paper presents an application of multiple tuned mass dampers (MTMDs) with non‐linear damping devices to suppress man‐induced vibrations of a 34m long pedestrian bridge. The damping force generated by each of these damping devices is simply a drag force from liquid acting on an immersed section. The quadratic non‐linear property of these devices was directly determined from free vibration tests of a simple laboratory set‐up. Dynamic models of the bridge and pedestrian loads were constructed for numerical investigation based on field measurement data. The control effectiveness of non‐linear MTMDs was examined along with its sensitivity against estimation errors in the bridge's natural frequency and magnitude of pedestrian load. The numerical results indicated that the optimum non‐linear MTMD system was as effective and robust as its linear counterpart. Then, a six‐unit non‐linear MTMD system was designed, constructed, and installed on the bridge. Field measurements after the installation confirmed the effectiveness of non‐linear MTMDs, and the measurement results were in good agreement with numerical predictions. After the installation, the average damping ratio of the bridge was raised from 0.005 to 0.036 and the maximum bridge accelerations measured during walking tests were reduced from about 0.80–1.30 ms−2 to 0.27–0.40 ms−2, which were within an acceptable range. Copyright © 2003 John Wiley & Sons, Ltd.
Oncostatin M enhances the expression of prostaglandin E2 and cyclooxygenase‐2 in astrocytes: Synergy with interleukin‐1β, tumor necrosis factor‐α, and bacterial lipopolysaccharide
Authors: Repovic Pavle , Mi Kaihong , Benveniste Etty N.
Published: April 2003

Oncostatin M (OSM), a cytokine of the interleukin‐6 family, is expressed in rheumatoid arthritis, multiple sclerosis, multiple myeloma, and other inflammatory and neoplastic conditions. Prostaglandin E2 (PGE2), an eicosanoid also associated with inflammation and cancer, has recently been shown to induce OSM expression. We report here that OSM in turn induces PGE2 production by astrocytes and astroglioma cells. More importantly, in combination with the inflammatory mediators IL‐1β, tumor necrosis factor‐α, and lipopolysaccharide, OSM exhibits a striking synergy, resulting in up to 50‐fold higher PGE2 production by astrocytes, astroglioma, and neuroblastoma cell lines. Enhanced PGE2 production by OSM and IL‐1β treatment is explained by their effect on cyclooxygenase‐2 (COX‐2), an enzyme that catalyzes the committed step in PGE2 synthesis. Of the enzymes involved in PGE2 biosynthesis, only COX‐2 mRNA and protein levels are synergistically amplified by OSM and IL‐1β. Nuclear run‐on assays demonstrate that OSM and IL‐1β synergistically upregulate transcription of the COX‐2 gene, and the mRNA stability assay indicates that COX‐2 mRNA is posttranscriptionally stabilized by OSM and IL‐1β. To effect synergy on the PGE2 level, OSM signals in part through its gp130/OSMRβ receptor, since neutralizing antibodies against gp130 and OSMRβ, but not LIFRβ, decrease PGE2 production in response to OSM plus IL‐1β. SB202190 and U0126, inhibitors of p38 MAPK and ERK1/2 activation, respectively, inhibit IL‐1β and OSM upregulation of COX‐2 and PGE2, indicating that these MAPK cascades are utilized by both stimuli. This mechanism of PGE2 amplification may be active in brain pathologies where both OSM and IL‐1β are present, such as glioblastomas and multiple sclerosis. GLIA 42:433–446, 2003. © 2003 Wiley‐Liss, Inc.
Early onset of degenerative changes at nodes of Ranvier in alpha‐motor axons of Cntf null (−/−) mutant mice
Authors: Gatzinsky Kliment P. , Holtmann Bettina , Daraie Babak , Berthold Claes‐Henric , Sendtner Michael
Published: April 2003

The nodes of Ranvier are sites of specific interaction between Schwann cells and axons. Besides their crucial role in transmission of action potentials, the nodes of Ranvier and in particular the paranodal axon‐Schwann cell networks (ASNs) are thought to function as local centers in large motor axons for removal, degradation, and disposal of organelles. In order to test whether ciliary neurotrophic factor (CNTF), which is present at high levels in the Schwann cell cytoplasm, is involved in the maintenance of these structures, we have examined lumbar ventral root nerve fibers of alpha‐motor neurons by electron microscopy in 3‐ and 9‐month‐old Cntf null (−/−) mutant mice. Nerve fibers and nodes of Ranvier in 3‐month‐old Cntf−/− mutants appeared morphologically normal, except that ASNs were more voluminous in the mutants than in wild‐type control animals at this age. In 9‐month‐old Cntf−/− animals, morphological changes, such as reduction in nerve fiber and axon diameter, myelin sheath disruption, and loss of ASNs at nodes of Ranvier, were observed. These findings suggest that endogenous CNTF, in addition to its role in promoting motor neuron survival and regeneration, is needed for long‐term maintenance of alpha‐motor nerve fibers. The premature loss of paranodal ASNs in animals lacking CNTF, which seems to be a defect related to a disturbed interaction in the nodal region between the axon and its myelinating Schwann cells, could impede the maintenance of a normal milieu in the motor axon, preceding more general neuronal damage. GLIA 42:340–349, 2003. © 2003 Wiley‐Liss, Inc.