bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualizing Phylogenetic Trees Using TreeView
Authors: Page Roderic D.M.
Published: June 2004

TreeView provides a simple way to view the phylogenetic trees produced by a range of programs, such as PAUP*, PHYLIP, TREE‐PUZZLE, and ClustalX. While some phylogenetic programs (such as the Macintosh version of PAUP*) have excellent tree printing facilities, many programs do not have the ability to generate publication quality trees. TreeView addresses this need. The program can read and write a range of tree file formats, display trees in a variety of styles, print trees, and save the tree as a graphic file. Protocols in this unit cover both displaying and printing a tree. Support protocols describe how to download and install TreeView, and how to display bootstrap values in trees generated by ClustalX and PAUP*.
Getting a Tree Fast: Neighbor Joining and Distance‐Based Methods
Authors: Gascuel Olivier
Published: June 2004

This unit provides instructions on how to construct a phylogenetic tree with several distance‐based methods. Neighbor Joining (NJ) and other distance‐based approaches (e.g., BIONJ, WEIGHBOR and FITCH) are fast methods for building phylogenetic trees. This makes them particularly effective for large‐scale studies or for bootstrap applications, which require runs on multiple data sets. Like maximum‐likelihood methods, distance methods are based on a sequence evolution model that is used to estimate the distance matrix. Computer simulations indicate that the topological accuracy of BIONJ, WEIGHBOR and FITCH is significantly better than that of NJ, and that the best distance‐based methods are equivalent to parsimony in most cases.
Maximum‐Likelihood Analysis Using TREE‐PUZZLE
Authors: Schmidt Heiko A. , von Haeseler Arndt
Published: June 2004

TREE‐PUZZLE provides means to analyze and reconstruct evolutionary relationships and trees based on quartets, i.e. groups of 4 sequences. explains how to reconstruct trees based on the maximum‐likelihood principle and quartet puzzling. discusses likelihood mapping, a method to visualize phylogenetic content in a multiple sequence alignment. explains how to compare tree topologies using different tests.
What If I Don't Have a Tree?: Split Decomposition and Related Models
Authors: Huson Daniel H.
Published: June 2004

A set of aligned character sequences or a matrix of evolutionary distances often contains a number of different and sometimes conflicting phylogenetic signals, and thus does not always support a unique tree. The method of split decomposition addresses this problem. For ideal data, this method gives rise to a phylogenetic tree, whereas less ideal data are represented by a tree‐like network that may indicate evidence of different and conflicting phylogenies. The SplitsTree program, described here, implements this approach and can be used to compute and visualize phylogenetic networks called splits graphs. It also implements a number of distance transformations, the computation of parsimony splits, spectral analysis and bootstrapping.
Using PEBBLE for the Evolutionary Analysis of Serially Sampled Molecular Sequences
Authors: Goode Matthew , Rodrigo Allen G.
Published: June 2004

The PEBBLE (Phylogenetics, Evolutionary Biology, and Bioinformatics in a moduLar Environment) application is a relative newcomer to the field of phylogenetic applications. Although designed as a customizable generalist application, PEBBLE was initially developed to implement procedures for the analysis of sequences associated with different sampling times, e.g., rapidly evolving viral genes sampled over the course of infection, or ancient DNA sequences. The basic protocol describes the use of PEBBLE to infer a phylogenetic tree using the sUPGMA algorithm, and the inference of substitution rate parameters using maximum likelihood. The alternate and support protocols describe the simulation capabilities of PEBBLE, and general use of the PEBBLE application, respectively.
Analysis of Expression Data: An Overview
Authors: Grewal Anoop , Lambert Peter , Stockton Jordan
Published: June 2004

After providing a brief introduction to microarray chips and experimental details, this overview discusses analysis techniques. Data analysis from microarray experiments generally involves two parts: acquiring and normalizing the data, and interpreting it. This unit focuses mostly on the latter, as it is less technology‐specific.
The Gene Ontology (GO) Project: Structured Vocabularies for Molecular Biology and Their Application to Genome and Expression Analysis
Authors: Blake Judith A. , Harris Midori A.
Published: June 2004

Scientists wishing to utilize genomic data have quickly come to realize the benefit of standardizing descriptions of experimental procedures and results for computer‐driven information retrieval systems. The focus of the Gene Ontology project is three‐fold. First, the project goal is to compile the Gene Ontologies; structured vocabularies describing domains of molecular biology. Second, the project supports the use of these structured vocabularies in the annotation of gene products. Third, the gene product‐to‐GO annotation sets are provided by participating groups to the public through open access to the GO database and Web resource. This unit describes the current ontologies and what is beyond the scope of the Gene Ontology project. It addresses the issue of how GO vocabularies are constructed and related to genes and gene products. It concludes with a discussion of how researchers can access, browse, and utilize the GO project in the course of their own research.
Analysis of Gene‐Expression Data Using J‐Express
Authors: Jonassen Inge , Dysvik Bjarte
Published: June 2004

The J‐Express package has been designed to facilitate the analysis of microarray data with an emphasis on efficiency, usability, and comprehensibility. The J‐Express system provides a powerful and integrated platform for the analysis of microarray gene expression data. It is platform independent in that it requires only the availability of a Java virtual machine on the system. The system includes a range of analysis tools and a project management system supporting the organization and documentation of an analysis project. This unit describes the J‐Express tool emphasizing central concepts and principles, and gives examples of how it can be used to explore gene expression data sets.
DRAGON and DRAGON View: Information Annotation and Visualization Tools for Large‐Scale Expression Data
Authors: Bouton Christopher M.L.S. , Pevsner Jonathan
Published: June 2004

The Database Referencing of Array Genes ONline (DRAGON) database system consists of information derived from publicly available databases including UniGene, SWISS‐Prot, Pfam, and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Through a Web‐accessible interface, the DRAGON Annotate tool rapidly supplies information pertaining to a range of biological characteristics of all the genes in any large‐scale gene expression data set. The subsequent inclusion of this information during data analysis and visualization allows for deeper insight into gene expression patterns. The set of DRAGON View tools provides methods for the analysis and visualization of expression patterns in relation to annotated information. Instead of incorporating the standard set of clustering and graphing tools available in many large‐scale expression data analysis software packages, DRAGON View has been specifically designed to allow for the analysis of expression data in relation to the biological characteristics of gene sets.
Using GenMAPP and MAPPFinder to View Microarray Data on Biological Pathways and Identify Global Trends in the Data
Authors: Dahlquist Kam D.
Published: June 2004

GenMAPP (Gene MicroArray Pathway Profiler) is a free, stand‐alone computer program designed for viewing and analyzing gene expression data on MAPPs representing biological pathways or any other functional grouping of genes. A MAPP is a special file format produced with the graphics tools in GenMAPP that depicts the biological relationship between genes or gene products. When a MAPP is linked to an expression dataset, GenMAPP automatically and dynamically color‐codes the genes on the MAPP according to criteria supplied by the user. MAPPFinder is an accessory program that works with GenMAPP and the annotations from the Gene Ontology (GO) Consortium to identify global biological trends in gene expression data. MAPPFinder relates the microarray dataset to the GO hierarchy and calculates a percentage and statistical score for genes meeting the user's criterion for a meaningful gene expression change for each GO biological process, cellular component, and molecular function term.
Integrating Whole‐Genome Expression Results into Metabolic Networks with Pathway Processor
Authors: Cavalieri Duccio , Grosu Paul
Published: June 2004

Genes never act alone in a biological system, but participate in a cascade of networks. As a result, analyzing microarray data from a pathway perspective leads to a new level of understanding the system. The authors' group has recently developed Pathway Processor (http://cgr.harvard.edu/cavalieri/pp.html), an automatic statistical method to determine which pathways are most affected by transcriptional changes and to map expression data from multiple whole‐genome expression experiments on metabolic pathways. This unit presents applications of the Pathway Processor software.
Prediction of Protein‐Protein Interaction Networks
Authors: Gomez Shawn M.
Published: June 2004

This unit offers a general overview of several techniques that have been developed for inferring functional and/or protein‐protein interaction networks. The majority of these use whole‐genome sequences as their primary input source of data. In addition, a few methods that utilize both protein features and experimental protein‐protein interaction data directly in the prediction of new interactions have recently been developed. As a result, a slightly more detailed description of one such method is also provided. While not an exhaustive list of approaches, it is hoped that the reader will gain a sense of how these approaches are implemented, an idea of their relative strengths and weaknesses, as well as some perspective on the type of work being conducted in this highly active area of research.
Evaluation of Electrostatic Interactions
Authors: Green David F. , Tidor Bruce
Published: June 2004

Described here are several computational procedures for the analysis of electrostatic interactions in molecular complexes, all based on a continuum model of solvation. The first section describes how to compute the residual potential, a measure of how electrostatically complementary a ligand is for its receptor. The second procedure describes electrostatic component analysis, a method by which the electrostatic contribution to the binding free energy can be broken up into terms directly attributable to individual chemical groups. Finally, electrostatic affinity optimization is described. This procedure is particularly useful in determining what portions of a ligand are the most suboptimal, and thus provide the greatest opportunity for the design of improvements.
Using DelPhi to Compute Electrostatic Potentials and Assess Their Contribution to Interactions
Authors: Oron Assaf , Wolfson Haim , Gunasekaran Kannan , Nussinov Ruth
Published: June 2004

There is a general agreement that electrostatic interactions play a significant role in the structure and function of biological molecules. However, obtaining quantitative estimation of the electrostatic energy requires computational models that capture the microscopic nature of the heterogeneous environment of macromolecules. This protocol offers elaboration on one of the common methods to calculate the electrostatic energetic contributions using continuum electrostatics. The method involves solving the Poisson‐Boltzmann (PB) equation numerically and regarding the solute as having a homogenous dielectric constant. In order to apply this method, a three dimensional structure of the molecule derived from experimental data (crystallography, NMR) or modeling techniques is required. The protocol will focus on the DelPhi program (Accelrys Inc. San Diego), which is one of the most common programs used for the estimation of electrostatic free energy contribution. A simple procedure of assigning criteria and parameters (charge distribution, solvent and solute dielectric constants, iterations, grid resolution, etc) enables one to illustrate an electrostatic potential map and estimate the electrostatic free energy, although with limited accuracy.
Searching the MINT Database for Protein Interaction Information
Authors: Cesareni Gianni , Helmer‐Citterich Manuela
Published: June 2004

The Molecular Interactions Database (MINT) is a relational database designed to store information about protein interactions. Expert curators extract the relevant information from the scientific literature and deposit it in a computer readable form. Currently (April 2003) MINT contains information on 4300 proteins and >3000 interactions. Although MINT contains interactions among proteins for several different species, the curators have initially focused on protein interactions in mammalian species. Protocols are provided here for searching MINT over the Internet, using the MINT Viewer.
Creating Databases for Biological Information: An Introduction
Authors: Stein Lincoln
Published: June 2004

The essence of bioinformatics is dealing with large quantities of information. Whether it be sequencing data, microarray data files, mass spectrometric data (e.g., fingerprints), the catalog of strains arising from an insertional mutagenesis project, or even large numbers of PDF files, there inevitably comes a time when the information can simply no longer be managed with files and directories. This is where databases come into play. This unit briefly reviews the characteristics of several database management systems, including flat file, indexed file, and relational databases, as well as ACeDB. It compares their strengths and weaknesses and offers some general guidelines for selecting an appropriate database management system.
Structured Query Language (SQL) Fundamentals
Authors: Jamison D. Curtis
Published: June 2004

Relational databases provide the most common platform for storing data. The Structured Query Language (SQL) is a powerful tool for interacting with relational database systems. SQL enables the user to concoct complex and powerful queries in a straightforward manner, allowing sophisticated data analysis using simple syntax and structure. This unit demonstrates how to use the MySQL package to build and interact with a relational database.
Modeling Biology Using Relational Databases
Authors: Peitzsch Robert M.
Published: June 2004

There are several different methodologies that can be used for designing a database schema; no one is the best for all occasions. This unit demonstrates two different techniques for designing relational tables and discusses when each should be used. These two techniques presented are (1) traditional Entity‐Relationship (E‐R) modeling and (2) a hybrid method that combines aspects of data warehousing and E‐R modeling. The method of choice depends on (1) how well the information and all its inherent relationships are understood, (2) what types of questions will be asked, (3) how many different types of data will be included, and (4) how much data exists.
Viewing and Editing Assembled Sequences Using Consed
Authors: Gordon David
Published: June 2004

Consed is a program for viewing and editing assemblies prepared by the Phrap assembly program. This unit presents a general introduction to Consed. It also provides instructions for identifying problem regions and searching in Consed. Additional protocols describe creating tags, picking primers, correcting joins and adding and removing reads. Instructions are also given for the use of Assembly View, predicting the results of a restriction digestion, the use of Consed in conjunction with PolyPhred, and using Autofinish, as well as a procedure for running Phred and Phrap.
Common File Formats
Authors: Leonard Shonda A. , Littlejohn Timothy G.
Published: June 2004

This appendix discusses a few of the file formats frequently encountered in bioinformatics. Specifically, it reviews the rules for generating FASTA files and provides guidance for interpreting NCBI descriptor lines, commonly found in FASTA files. In addition, it reviews the construction of GenBank files.
Unix Survival Guide
Authors: Stein Lincoln D.
Published: June 2004

For a mixture of historical and practical reasons, much of the bioinformatics software discussed in this series runs on Linux, Mac OS X, Solaris, or one of the many other Unix variants. This appendix provides the novice with easy‐to‐understand information needed to survive in the Unix environment.
X Window Survival Guide
Authors: Stein Lincoln D.
Published: June 2004

Logging‐in to a Unix system from a console typically initiates a graphical desktop environment that is similar to the Microsoft Windows and Apple Macintosh desktops. Logging‐in remotely to a Unix system, however, typically limits the user to a small text‐only window, which is unable to launch graphical applications. This appendix describes the two main options for overcoming this obstacle: a Virtual Network Computer (VNC) and the X Window System.
Optimization algorithms for bilinear model–based predictive control problems
Authors: Bloemen H. H. J. , van den Boom T. J. J. , Verbruggen H. B.
Published: June 2004

Model‐based predictive control (MPC) for discrete‐time bilinear state–space models is considered. The optimization problem of the bilinear MPC algorithm is nonlinear in general. It is demonstrated that the structural properties of the bilinear state–space model provide a way to formulate the nonlinear optimization problem as a sequence of quadratic programming problems that exactly represent the original objective function. The proposed optimization algorithm is compared to one that is based on a linearization about an input trajectory. To benefit from the advantages of both algorithms, a hybrid algorithm is proposed, which outperforms the other two in most cases. The applicability of the proposed bilinear MPC algorithm is demonstrated on a polymerization process. 2004 American Institute of Chemical Engineers AIChE J, 50:1453–1461, 2004
Anogenital gland secretions of Lemur catta and Propithecus verreauxi coquereli: A preliminary chemical examination
Authors: Hayes R.A. , Morelli T.L. , Wright P.C.
Published: June 2004

Although prosimians are greatly olfaction‐oriented, little is known about the specifics of how they use scent to communicate. In this preliminary study we attempted to delineate intra‐ and interspecific differences among the anogenital gland secretions of two lemur species (Lemur catta and Propithecus verreauxi coquereli) using gas chromatography‐mass spectrometry (GC‐MS). The results indicate that the two species are discernible through scent. Furthermore, we were able to identify reproductive status using this technique. The anogenital secretions of the different sexes in L. catta, though perhaps not P. v. coquereli, are chemically distinguishable. Given this information, it appears that at least some lemur species can use scent marks to determine species, sex, and reproductive status. Am J Primatol 63:49–62, 2004. © 2004 Wiley‐Liss, Inc.
Pre‐retirement predator encounters alter the morning behavior of captive marmosets (Callithrix geoffroyi)
Authors: Hankerson Sarah J. , Caine Nancy G.
Published: June 2004

Limited data are available on the long‐term effect an encounter with a predator has on its potential prey. Anecdotal reports from field research indicate that even unsuccessful attacks by predators on callitrichids have long‐lasting effects. The subjects for this study were two groups of Geoffroy's marmosets (Callithrix geoffroyi) housed outside, off exhibit, at the Center for Reproduction of Endangered Species at the San Diego Wild Animal Park. Before they retired in the evening, the marmosets were observed under one of three conditions: snake model, cloth control, and no‐stimulus control. Data were collected the following morning for 1 hr after the animals emerged from the sleeping box. Compared to control conditions, exposure to the snake model before retirement the previous evening was associated with significantly more vigilance checks (i.e., inspecting the area where the stimulus was last seen), and a delay in beginning to forage on the ground. These results suggest that callitrichids use recent threatening experiences to guide their vigilance behavior 12 hr after the threat is detected, and that they adjust their early morning behavior in response to potential predatory threats. Am. J. Primatol. 63:75–85, 2004. © 2004 Wiley‐Liss, Inc.
Nonphosphorylated high‐molecular‐weight neurofilament expression suggests early maturation of the monkey subiculum
Authors: Lavenex Pierre , Lavenex Pamela Banta , Amaral David G.
Published: June 2004

We analyzed the distribution of nonphosphorylated high‐molecular‐weight neurofilaments (NF‐H) in the hippocampal formation of infant (3‐week‐old and 3‐month‐old) and adult (9–17‐year‐old) macaque monkeys in order to obtain neuroanatomical evidence of the maturity of these structures shortly after birth. We employed the monoclonal antibody SMI‐32, a well‐characterized antibody raised against nonphosphorylated NF‐H, the expression of which is believed to reflect the maturation of certain neuronal populations. Patterns of SMI‐32 immunoreactivity differed dramatically between infant and adult monkeys. In adults, nonphosphorylated NF‐H expression was prominent in the CA3 and CA2 fields of the hippocampus, in the subiculum and in the entorhinal cortex. In infants, only the subiculum stained heavily for nonphosphorylated NF‐H. These findings suggest that different subregions of the primate hippocampal formation mature at different times during development. The subiculum, the major source of efferent projections from the hippocampal formation toward subcortical structures, matures early during development. In contrast, the entorhinal cortex, the main interface of the hippocampal formation with the neocortex, matures relatively later. These findings have direct implications for the type of information processing that might be subserved by the primate hippocampal formation shortly after birth, as well as for the emergence of particular behavioral and memory processes during postnatal development. © 2004 Wiley‐Liss, Inc.
Biodegradable radiation delivery system utilizing glass microspheres and ethylenediaminetetraacetate chelation therapy
Authors: Conzone Samuel D. , Hall Matthew M. , Day Delbert E. , Brown Roger F.
Published: June 2004

Dysprosium lithium‐borate (DyLB) glass microspheres have been developed as a biodegradable radiation delivery vehicle for the treatment of rheumatoid arthritis and other diseases. Radioactive microspheres of these glasses are intended to be injected into a joint infected with rheumatoid arthritis to safely deliver a localized dose (100 Gy) of beta radiation. Once injected, the microspheres react nonuniformly with body fluids. The nonradioactive, lithium‐borate component is dissolved from the glass, whereas the radioactive 165Dy reacts with phosphate anions in the body fluids, and becomes “chemically” trapped in a solid, dysprosium phosphate reaction product that has the same size as the unreacted microsphere. The glass microspheres lose ≈80% of their weight after nonuniform reaction (<1 day), but the dysprosium phosphate reaction product is slowly metabolized by the body over several months. Ethylenediaminetetraacetate (EDTA) chelation therapy can be used to dissolve the dysprosium phosphate reaction product in vitro in <2 h. The dysprosium phosphate reaction product which formed in vivo in the joint of a Sprague‐Dawley rat was also dissolved by EDTA chelation therapy in <1 week, without causing any detectable joint damage. The combination of DyLB glass microspheres and EDTA chelation therapy provides a unique “tool” for the medical community because it can deliver a large dose (>100 Gy) of localized beta radiation to a treatment site within the body, followed by complete biodegradability. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res 70A: 256–264, 2004
Alterations of cell lipids by metal salts
Authors: Schuster George S. , Caughman Gretchen B.
Published: June 2004

Metallic medical devices undergo degradation in vivo and the degradation products affect the chemistry and biological responses of cells and tissues in the immediate vicinity. The responses vary with the metal and cell type. In the current study, we examined the effects of several metals on a human monocytic cell line. Monocytes are important effector cells capable of responding rapidly to inflammatory and immune stimuli in a variety of ways, including production of inflammatory proteins, differential expression of surface adhesion molecules, enhanced phagocytic activity, and activation and differentiation to macrophages. Cells were exposed in the presence of 14C‐acetate to titanium, nickel, chromium, copper, or cobalt or vanadium at concentrations that were subinhibitory or inhibitory based on cellular mitochondrial dehydrogenase activity. Cell lipids were then extracted, separated by thin layer chromatography, and quantitated by liquid scintillation spectrometry. Total cell protein also was measured. Titanium reduced cell protein content at concentrations that were noninhibitory to mitochondrial dehydrogenase activity, whereas neither chromium nor cobalt affected protein amounts at dehydrogenase‐inhibitory concentrations. In cells exposed to vanadium, the protein‐ and dehydrogenase‐inhibitory concentrations were similar. The major effects on cell lipids appeared to occur in the neutral lipids, although chromium, cobalt, and titanium produced changes in some major phospholipids. These results suggest that metals differentially affect various metabolic pathways in THP‐1 cells, perhaps related to their abilities to enter the cells or interact with the membrane. These alterations to the cells may affect the cells' abilities to respond to various stimuli that can damage the tissues. © 2004 Wiley Periodicals, Inc. J Biomed Mater Res 70A: 347–353, 2004
Characterization of non‐covalent complexes of rutin with cyclodextrins by electrospray ionization tandem mass spectrometry
Authors: Guo Mingquan , Song Fengrui , Liu Zhiqiang , Liu Shuying
Published: June 2004

Electrospray ionization tandem mass spectrometry (ESI‐MSn) and the phase solubility method were used to characterize the gas‐phase and solution‐phase non‐covalent complexes between rutin (R) and α‐, β‐ and γ‐cyclodextrins (CDs). The direct correlation between mass spectrometric results and solution‐phase behavior is thus revealed. The order of the 1 : 1 association constants (Kc) of the complexes between R and the three CDs in solution calculated from solubility diagrams is in good agreement with the order of their relative peak intensities and relative collision‐induced dissociation (CID) energies of the complexes under the same ESI‐MSn condition in both the positive and negative ion modes. Not only the binding stoichiometry but also the relative stabilities and even binding sites of the CD–R complexes can be elucidated by ESI‐MSn. The diagnostic fragmentation of CD–R complexes, with a significant contribution of covalent fragmentation of rutin leaving the quercetin (Q) moiety attached to the CDs, provides convincing evidence for the formation of inclusion complexes between R and CDs. The diagnostic fragment ions can be partly confirmed by the complexes between Q and CDs. The gas‐phase stability order of the deprotonated CD–R complexes is β‐CD–R > α‐CD–R > γ‐CD/R; β‐CD seems to bind R more strongly than the other CDs. Copyright © 2004 John Wiley & Sons, Ltd.
Screening for dihydropyridine calcium channel blockers in plasma by automated solid‐phase extraction and liquid chromatography/tandem mass spectrometry
Authors: Mueller Claudia A. , González Ana B. Baranda , Weinmann Wolfgang
Published: June 2004

A liquid chromatographic/tandem mass spectrometric (LC/MS/MS) screening method was developed for the screening of 11 calcium channel blockers of the 1,4‐dihydropyridine type in plasma samples for forensic and clinical cases. Plasma samples were extracted by automated solid‐phase extraction. Analysis was performed using a reversed‐phase C18 column, gradient elution and a triple‐quadrupole mass spectrometer with TurboIonSpray source in positive mode and multiple reaction monitoring. This method was found to be selective and sensitive for the detection of the target compounds at their therapeutic plasma concentrations. Copyright © 2004 John Wiley & Sons, Ltd.
Site of alkylation of N‐methyl‐ and N‐ethylaniline in the gas phase: a tandem mass spectrometric study
Authors: Ackloo Suzanne , Harrison Alex G. , Terlouw Johan K.
Published: June 2004

N‐Methylaniline (NMA) was ethylated and N‐ethylaniline (NEA) was methylated under chemical ionization conditions using C2H5I and CH3I, respectively, as reagent gases. The structures of the resulting m/z 136 adduct ions have been probed using metastable ion and collision‐induced dissociation (CID) methods. From the similarity of the spectra obtained and from the presence of structure‐diagnostic ions at m/z 59 (CH3NHC2H5+•) and m/z 44 (CH3NHCH2+), it is concluded that predominantly N‐alkylation occurs in both systems. This interpretation was aided by the use of C2D5I and CD3I as reagents. Adduct ions of m/z 136 were also formed by ethylation of the isomeric toluidines and by methylation of the ring‐ethylanilines. The resulting CID mass spectra were distinctly different from those obtained for the m/z 136 ions obtained by alkylation of NMA and NEA. Protonation of N‐ethyl‐N‐methylaniline using CH3C(O)CH3 as Brønsted acid reagent produced an m/z 136 species whose CID mass spectrum also featured intense ion signals at m/z 59 and 44. This observation led to the conclusion that protonation with acetone as reagent results, in this case, in dominant N‐protonation. However, the CID mass spectrum of the m/z 136 ion formed when CH3OH was the protonating agent featured a weak signal at m/z 44 and no signal at m/z 59. Hence it was concluded that the latter m/z 136 ion contains a larger contribution from the ring‐protonated adduct. Copyright © 2004 John Wiley & Sons, Ltd.
Isolation of retinal progenitor cells from post‐mortem human tissue and comparison with autologous brain progenitors
Authors: Klassen Henry , Ziaeian Boback , Kirov Ivan I. , Young Michael J. , Schwartz Philip H.
Published: June 2004

The goal of the present study was threefold: to determine whether viable human retinal progenitor cells (hRPCs) could be obtained from cadaveric retinal tissue, to evaluate marker expression by these cells, and to compare hRPCs to human brain progenitor cells (hBPCs). Retinas were dissected from post‐mortem premature infants, enzymatically dissociated, and grown in the presence of epidermal growth factor and basic fibroblast growth factor. The cells grew as suspended spheres or adherent monolayers, depending on culture conditions. Expanded populations were banked or harvested for analysis by RT‐PCR, immunocytochemistry, and flow cytometry. hBPCs derived from forebrain specimens from the same donors were grown and used for RT‐PCR. Post‐mortem human retinal specimens yielded viable cultures that grew to confluence repeatedly, although not beyond 3 months. Cultured hRPCs expressed a range of markers consistent with CNS progenitor cells, including nestin, vimentin, Sox2, Ki‐67, GD2 ganglioside, and CD15 (Lewis X), as well as the tetraspanins CD9 and CD81, CD95 (Fas), and MHC class I antigens. No MHC class II expression was detected. hRPCs, but not hBPCs, expressed Dach1, Pax6, Six3, Six6, and recoverin. Minority subpopulations of hRPCs and hBPCs expressed doublecortin, β‐III tubulin, and glial fibrillary acidic protein, which is consistent with increased lineage restriction in subsets of cultured cells. Viable progenitor cells can be cultured from the post‐mortem retina of premature infants and exhibit a gene expression profile consistent with immature neuroepithelial cells. hRPCs can be distinguished from hBPC cultures by the expression of retinal specification genes and recoverin. © 2004 Wiley‐Liss, Inc.
Three putative N‐glycosylation sites within the murine 5‐HT3A receptor sequence affect plasma membrane targeting, ligand binding, and calcium influx in heterologous mammalian cells
Authors: Quirk Phillip L. , Rao Suma , Roth Bryan L. , Siegel Ruth E.
Published: June 2004

The serotonin type 3A receptor (5‐HT3AR) is a ligand‐gated ion channel (LGIC) that modulates a diverse set of cognitive and physiological functions. The 5‐HT3AR, as with other LGICs, is a pentameric ion channel comprising five glycoprotein subunits. Although the N‐terminal of the 5‐HT3AR contains three putative N‐linked glycosylation sites, the importance of each glycosylation site has not yet been established. To address this question, we used tunicamycin treatment and site‐directed mutagenesis to inhibit selectively N‐linked glycosylation at each site and then examined the effects of these treatments on receptor expression and function in transiently transfected heterologous cells. We show that the murine 5‐HT3AR is glycosylated and that each N‐linked glycosylation site plays a role in receptor regulation. Our findings suggest that N109 is necessary for receptor assembly, whereas N174 and N190 are important for plasma membrane targeting and ligand binding. Furthermore, we demonstrate that each site is necessary for 5‐HT3AR‐mediated Ca2+ influx. We conclude that N‐glycosylation is a critical step in the maturation, trafficking, and function of the murine 5‐HT3AR. © 2004 Wiley‐Liss, Inc.
Steady plasma concentration of unfractionated heparin reduces infarct volume and prevents inflammatory damage after transient focal cerebral ischemia in the rat
Authors: Cervera Álvaro , Justicia Carles , Reverter Joan C. , Planas Anna M. , Chamorro Ángel
Published: June 2004

Unfractionated heparin (UH) decreases the extent of infarction after transient focal brain ischemia in the rat and abridges neuroinflammatory damage in patients with acute stroke. This study was aimed at assessing whether controlled and steady heparinemia in plasma can reduce infarct volume and exert neuroprotective effects after ischemia. Infarct volume was measured at 24 and 7 days following a 1‐hr intraluminal middle cerebral artery (MCA) occlusion in rats treated with UH or with vehicle. After testing several UH administration protocols, we choose to give a bolus of 200 U/kg, which was started 3 hr after the occlusion, followed by a 24‐hr intraperitoneal perfusion of 70 U/kg/hr, which maintained a 24‐hr steady plasma heparinemia (0.3–0.6 U/ml) and caused no CNS or systemic bleeding. In addition, plasma IL‐10 concentration was measured by ELISA, endothelial VCAM‐1 expression was evaluated by i.v. injection of a 125I‐labeled monoclonal antibody against VCAM‐1, and brain hemeoxygenase‐1 (HO‐1) expression was determined by Western blot. UH‐treated rats showed smaller infarctions than rats treated with vehicle, as well as higher IL‐10 plasma levels and HO‐1 brain expression and lower endothelial VCAM‐1 induction. The study shows that a stable plasma concentration of UH given at nonhemorrhagic doses reduces infarct volume after ischemia‐reperfusion in the rat. It also shows that UH prevented the induction of cell adhesion molecules in the cerebral vasculature and increased the expression of molecules with antiinflammatory and prosurvival properties. These findings support further testing of the clinical value of parenteral, adjusted, high‐dose UH in patients with acute stroke. © 2004 Wiley‐Liss, Inc.
Expression and location of mRNAs encoding multiple forms of secretory phospholipase A2 in the rat retina
Authors: Kolko Miriam , Christoffersen Nanna R. , Barreiro Sebastian G. , Bazan Nicolas G.
Published: June 2004

Low‐molecular‐weight secretory phospholipases A2 (sPLA2s) are a subgroup of PLA2s, which are secreted, bind to receptors, and may act as intercellular signaling modulators. At least 10 different groups have been characterized in mammals, and there is expanding evidence of the significance of sPLA2s in neuronal signaling and survival [Kolko et al. (1996) J. Biol. Chem. 271: 32722–32728]. To date, no retinal sPLA2s have been cloned or characterized. We evaluated the existence and abundance of sPLA2 subtypes in rat retina and explored their possible involvement in light‐induced retinal damage. We designed primers to identify the sPLA2s in rat retina, based on known sequences of sPLA2‐specific mRNAs in other tissues. RNA was isolated from rat retina, and cDNA was produced and used for PCR cloning to identify the novel subtypes of sPLA2. Our study revealed the presence of mRNAs encoding sPLA2‐IB, ‐X, ‐V, ‐IIE, ‐IIA, and ‐IIF in the retina, and quantification by real‐time PCR revealed different abundances of the sPLA2s. We showed a time‐dependent gene induction of sPLA2‐X, ‐IB, and ‐V in light‐induced retinal damage. We further explored the location of sPLA2‐IB by in situ hybridization and immunohistochemistry. This study is the first to reveal the presence, abundance, and induction of mRNAs encoding sPLA2s in rat retina. We suggest that these enzymes are themselves intercellular signaling modulators of retinal cell function and perhaps also of retinal degeneration. © 2004 Wiley‐Liss, Inc.
Synthesis and photoluminescence of linear and hyperbranched polyethers containing phenylquinoxaline units and flexible aliphatic spacers
Authors: Baek Jong‐Beom , Chien L.‐C.
Published: June 2004

Ultrahigh‐molecular‐weight linear polyethers were prepared through a reaction between the phenylquinoxaline monomers 2,3‐bis(4‐hydroxyphenyl)‐6‐fluoroquinoxaline and 2,3‐bis(4‐hydroxyphenyl)‐6‐(α,α,α‐trifluoromethyl)quinoxaline and 1,12‐dibromododecane. A new hyperbranched polyether containing a phenylquinoxaline moiety was also prepared from a new self‐polymerizable AB2 monomer, 2,3‐bis(6‐bromohexyloxyphenyl)‐6‐(4‐hydroxyphenyloxy)quinoxaline. All the polyethers were amorphous and soluble in polar aprotic solvents. Their solution‐cast thin films were light yellow, ductile, and optically transparent. The polymers were thermally stable up to 350 °C and had glass‐transition temperatures in the range of 25–83 °C, which depended on the architecture and monomer structure. The monomers and polymers displayed fluorescence maxima in the blue‐light region in the range of 431–449 nm with relatively narrow peak widths; this indicated that they had pure and intense fluorescence. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3587–3603, 2004
Macromolecular surfactants for supercritical carbon dioxide applications: Synthesis and characterization of fluorinated block copolymers prepared by nitroxide‐mediated radical polymerization
Authors: Lacroix‐Desmazes Patrick , Andre Pascal , Desimone Joseph M. , Ruzette Anne‐Valérie , Boutevin Bernard
Published: June 2004

Poly(perfluorooctyl‐ethylenoxymethylstyrene) (PFDS) and poly(1,1,2,2‐tetrahydroperfluorodecyl acrylate) (PFDA) homopolymers as well as poly(styrene)‐b‐poly(perfluorooctyl‐ethylenoxymethylstyrene) (PS‐b‐PFDS) and poly(styrene)‐b‐poly(1,1,2,2‐tetrahydroperfluorodecyl acrylate) acrylate) (PS‐b‐PFDA) block copolymers of various chain lengths were synthesized by nitroxide‐mediated radical polymerization in the presence of either 2,2,6,6‐tetramethyl‐1‐piperidinyloxy free radical (TEMPO) in the case of FDS monomer or N‐tert‐butyl‐N‐(1‐diethylphosphono‐2,2‐dimethylpropyl)‐N‐oxyl (DEPN) in the case of the FDA monomer. The molar composition of the block copolymers was determined by elemental analysis and proton NMR while the blocky structure was checked by SEC analysis in trifluorotoluene. Block copolymers PS‐b‐PFDS (3.6K/60K) and PS‐b‐PFDA (3.7K/43K) were soluble in neat CO2 at moderate pressure and temperature, indicating the formation of micelles. Similar block copolymers with a longer PS block such as PS‐b‐PFDA (9.5K/49K), corresponding to a lower CO2‐philic/CO2‐phobic balance, were insoluble in neat CO2 but could be solubilized in the presence of styrene as a cosolvent. Additionally, surface and bulk properties of PS‐b‐PFDA were investigated, indicating the same surface tension as for the PFDA homopolymer (γLV = 10.3 mN/m) and a bulk nanostructured morphology. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3537–3552, 2004
Kinetic modeling studies of ethylene polymerization reactions using supported chromium catalysts
Authors: Matos I. , Zhang Y. , Lemos M. A. N. D. A. , Freire Filipe , Fonseca I. F. , Marques M. M. , Lemos F.
Published: June 2004

Kinetic models for ethylene polymerization based on a general coordination–insertion mechanism, in which either a monocoordinated species or a bicoordinated species could lead to migratory insertion, were constructed. These models were implemented through the solution of a set of differential equations resulting from the material balances for all the species involved. The application of these kinetic models to monomer consumption for different supported catalysts produced very good fittings and allowed the estimation of the kinetic rate constants of each elementary step. Although the same kinetic scheme was used to describe all the observations, the results of the fitting showed that the supported chromium species behaved very differently according to the support. Only in the case of the silica‐supported catalysts was mechanical fragmentation of the particles observed during the course of the reaction, and this implied the inclusion of a new term in the model. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3464–3472, 2004
A new tetradentate ligand for atom transfer radical polymerization
Authors: Ding Shijie , Shen Youqing , Radosz Maciej
Published: June 2004

The properties of a ligand, including molecular structure and substituents, strongly affect the catalyst activity and control of the polymerization in atom transfer radical polymerization (ATRP). A new tetradentate ligand, N,N′‐bis(pyridin‐2‐ylmethyl‐3‐hexoxo‐3‐oxopropyl)ethane‐1,2‐diamine (BPED) was synthesized and examined as the ligand of copper halide for ATRP of styrene (St), methyl acrylate (MA), and methyl methacrylate (MMA), and compared with other analogous linear tetrdendate ligands. The BPED ligand was found to significantly promote the activation reaction: the CuBr/BPED complex reacted with the initiators so fast that a large amount of Cu(II)Br2/BPED was produced and thus the polymerizations were slow for all the monomers. The reaction of CuCl/BPED with the initiator was also fast, but by reducing the catalyst concentration or adding CuCl2, the activation reaction could be slowed to establish the equilibrium of ATRP for a well‐controlled living polymerization of MA. CuCl/BPED was found very active for the polymerization of MA. For example, 10 mol% of the catalyst relatively to the initiator was sufficient to mediate a living polymerization of MA. The CuCl/BPED, however, could not catalyze a living polymerization of MMA because the resulting CuCl2/BPED could not deactivate the growing radicals. The effects of the ligand structures on the catalysis of ATRP are also discussed. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3553–3562, 2004
Accuracy of absence of fetal breathing movements in predicting preterm birth: a systematic review
Authors: Honest H. , Bachmann L. M. , Sengupta R. , Gupta J. K. , Kleijnen J. , Khan K. S.
Published: June 2004

Objective

To determine the accuracy with which the absence of fetal breathing movements on ultrasound examination predicts spontaneous preterm birth in women with threatened preterm labor.

Methods

Data sources included Medline, Embase, Pascal, Biosis, Cochrane Library, Medion, National Research Register, SciSearch, conference papers, and manual searching of bibliographies of known primary and review articles. A study was selected if it used absence of fetal breathing movements on ultrasound to predict spontaneous preterm birth in women with threatened preterm labor but before advanced cervical dilatation. Two reviewers independently selected studies and extracted data on their characteristics, quality and accuracy. Accuracy data were used to form 2 × 2 contingency tables with birth within 48 h and within 7 days of testing as the reference standards. Likelihood ratios for a positive test (LR+) and negative test (LR−) were calculated as a measure of accuracy.

Results

There were eight studies, which included a total of 328 women, evaluating the accuracy of absence of fetal breathing movements in predicting spontaneous preterm birth in women with threatened preterm labor. There were differences in the methodological quality among the included studies. All were lacking in one or more item that make up an ideal test accuracy study. For women presenting with threatened preterm labor, meta‐analysis showed a summary LR+ of 14.80 (95% CI, 6.30–34.79) with a corresponding summary LR− of 0.46 (95% CI, 0.36–0.58) for predicting preterm birth within 7 days, and summary LR+ of 7.84 (95% CI, 1.12–54.99) and summary LR− of 0.25 (95% CI, 0.13–0.48) for predicting preterm birth within 48 h of testing.

Conclusion

Absence of fetal breathing movements has the potential to be a useful test in predicting preterm birth both within 7 days and within 48 h of testing. However, the available studies were deficient in their sample size and quality of methodology. Future research should be undertaken to evaluate this technology and to address the methodological deficiencies. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Impaired endothelium‐dependent and ‐independent vasodilation in elderly patients with chronic heart failure
Authors: Morgan David R. , Dixon Lana J. , Hanratty Colm G. , Hughes Sinead M.T. , Leahey William J. , Rooney Keith P. , Johnston G. Dennis , McVeigh Gary E.
Published: June 2004

Background:

Impaired endothelium‐dependent and independent vasodilator responses in chronic heart failure (CHF) have been well described. Previous studies involved younger patients and omitted medications prior to study.

Aims:

We explored if new therapeutic interventions would restore vasodilator responses in typical patients with chronic heart failure.

Methods and results:

24 patients and 15 controls were recruited, patients were maintained on their usual medications. Forearm blood flow responses were measured by venous occlusion plethysmography in response to incremental doses of sodium nitroprusside (SNP) (6, 9 and 12 nmol/min), acetylcholine (ACH) (120, 180 and 240 nmol/min), angiotensin II (AII) (1, 10 and 100 nmol/min) and Ng‐Nitro‐l‐arginine methyl ester (l‐NAME) (1, 2 and 4 nmol/min) infused into the non‐dominant brachial artery. FBF responses to SNP were impaired in patients compared with controls (13.7(9.9,17.4) vs. 24.8(18.6,30.9)) arbitrary units, P<0.001). Similarly FBF responses to ACH were reduced in patients compared with controls (7.5(4.2,10.9) vs. 24.8(16.4,33.2)) arbitrary units, P<0.001. Decreased FBF was noted in response to AII and l‐NAME but was significant only for AII and did not differ between groups.

Conclusions:

In elderly patients with CHF, endothelium‐dependent and independent vasodilator responses were blunted compared with controls. Defects in nitric oxide bioavailability and smooth muscle responsiveness are not reversed by modern medical management of the heart failure syndrome.