bluuebunny/crossref_metadata_2025 huggingface dataset:
Trade‐offs in community ecology: linking spatial scales and species coexistence
Authors: Kneitel Jamie M. , Chase Jonathan M.
Published: December 2003

Trade‐offs in species performances of different ecological functions is one of the most common explanations for coexistence in communities. Despite the potential for species coexistence occurring at local or regional spatial scales, trade‐offs are typically approached at a single scale. In recent years, ecologists have increasingly provided evidence for the importance of community processes at both local and regional spatial scales. This review summarizes the theoretical predictions for the traits associated with trade‐offs under different conditions and at different spatial scales. We provide a spatial framework for understanding trade‐offs, coexistence and the supportive empirical evidence. Predictions are presented that link the patterns of diversity observed to the patterns of trade‐offs that lead to coexistence at different spatial scales. Recent evidence for the evolution of trade‐offs under different conditions is provided which explores both laboratory microcosm studies and phylogenetic tests. Examining trade‐offs within a spatial framework can provide a strong approach to understanding community structure and dynamics, while explaining patterns of species diversity.
Ecological conditions during winter predict arrival date at the breeding quarters in a trans‐Saharan migratory bird
Authors: Saino Nicola , Szép Tibor , Romano Maria , Rubolini Diego , Spina Fernando , Møller Anders Pape
Published: December 2003

We studied variation in arrival date to the breeding colonies in Italy of a trans‐Saharan migratory bird, the barn swallowHirundo rustica, in relation to variation in ecological conditions, as reflected by the normalized difference vegetation index (NDVI), in the winter quarters. Arrival date of old but not young individuals captured during consecutive breeding seasons was earlier after winters with favourable conditions. Change in arrival date in relation to change in NDVI was similar in the two sexes. Change in arrival date significantly and positively predicted change in breeding date. As a result of increased frequency of second broods determined by earlier arrival, the number of fledged offspring per season was larger after African winters with good in comparison to poor ecological conditions for barn swallows. This is the first study demonstrating phenotypic plasticity in migration phenology of a long‐distance migratory bird in relation to ecological conditions during wintering.
A comprehensive framework for global patterns in biodiversity
Authors: Ricklefs Robert E.
Published: December 2003

The present study proposes to reconcile the different spatial and temporal scales of regional species production and local constraint on species richness. Although interactions between populations rapidly achieve equilibrium and limit membership in ecological communities locally, these interactions occur over heterogeneous environments within large regions, where the populations of species are stably regulated through competition and habitat selection. Consequently, exclusion of species from a region depends on long‐term regional‐scale environmental change or evolutionary change among interacting populations, bringing species production and extinction onto the same scale and establishing a link between local and regional processes.
Effects of moon phase and soak time on catches of Jasus (Sagmariasus) verreauxi recruits on collectors
Authors: Montgomery S. S. , Craig J. R.
Published: December 2003

The hypothesis tested in this study was that catches of recruits (sum of pueruli to early-stage juveniles of the same year class) of Jasus (Sagmariasus) verreauxi on seaweed-type collectors were affected by lunar periodicity and by the soak time of the collectors. Mean numbers of recruits did not differ between phases of the moon, but significantly more recruits were caught on collectors soaked for four weeks than on those soaked for three or two weeks, which in turn were greater than on those soaked for one week. On the basis of these results, it was recommended that collectors should be soaked for four weeks. This information was used in developing a uniform and optimal methodology for full surveys to monitor the relative abundance of recruits of J. verreauxi along the coast of New South Wales.
Diel habitat shifts of macrofauna in a fishless pond
Authors: Hampton Stephanie E. , Duggan Ian C.
Published: December 2003

Most studies of pond animals are undertaken during the daytime, despite evidence that many pond organisms demonstrate marked nocturnal changes in behaviour. Nocturnal studies of animals in fishless ponds are particularly rare, probably because diel changes in aquatic animal behaviour are often found to be a response to visual predation by fish. We used non-metric multidimensional scaling (MDS) and analysis of similarity (ANOSIM) to detect patterns of similarity in the community composition of macroinvertebrates and amphibians in samples taken from vegetated and unvegetated areas during the day and night in a fishless Vermont pond. We tested the hypotheses that (i) macrofaunal activity increased at night near the pond surface, and (ii) horizontal movement of the pond community was occurring on a diel cycle. At night, many taxa were more abundant in the surface waters and the community showed a general habitat expansion or shift from the littoral zone towards the edge and central waters. Our results challenge the assumptions that one would make about pond animal habitat use and interactions based solely on daytime studies. Even in fishless systems, where diel changes are unexpected, habitat use and behaviour might change at night and affect the strength and variety of species interactions.
Speciation and phylogeography in Caridina indistincta, a complex of freshwater shrimps from Australian heathland streams
Authors: Chenoweth Stephen F. , M.Hughes Jane
Published: December 2003

The Caridina indistincta complex is a group of closely related atyid shrimps that inhabit coastal freshwater streams throughout north-eastern Australia. Using mitochondrial DNA sequence data (cytochrome oxidase 1, CO1), we (1) inferred the timing of speciation in the C. indistincta group and (2) examined the intraspecific phylogeographic patterns within the group. Assuming a shrimp-specific rate of CO1 evolution, the level of sequence divergence among species suggests that speciation took place during the Miocene epoch. Within one widespread mainland species, phylogeographic patterns suggest strong geographic 'regionalisation' of mtDNA lineages that are most likely of Pleistocene origin. By contrast, another species comprises two highly divergent mtDNA lineages that occur in sympatry. We suggest that although Pleistocene sea-level regressions appear important in generating population-level phylogeographic patterns, these events were largely unimportant in the formation of species in this group.
Latitudinal variation in life-history traits of bonnethead sharks, Sphyrna tiburo, (Carcharhiniformes : Sphyrnidae) from the eastern Gulf of Mexico
Authors: Lombardi-Carlson Linda A. , Cortés Enric , Parsons Glenn R. , Manire Charles A.
Published: December 2003

Life-history traits (size at age, growth rates, size and age at maturity, size of near-term embryos and litter sizes) of bonnetheads, Sphyrna tiburo, were analysed to test for latitudinal differences by comparing data collected from three areas along Florida's Gulf of Mexico coastline between March 1998 and September 2000. A total of 539 sharks were collected during the study: 207 in north-west Florida (latitude ~30�N), 176 in Tampa Bay (~28�N) and 156 in Florida Bay (~25�N). Male and female bonnetheads in north-west Florida had the largest predicted asymptotic sizes (1007�mm and 1398�mm TL, respectively) and attained the largest estimated median size at maturity (830�mm and 944�mm, respectively) and the oldest estimated median age at maturity (3.0+�years and 4.0+�years, respectively). The largest near-term embryos (297�mm TL) were also collected at the highest latitude, but no latitudinal difference in litter size was found. These differences in life-history traits provide supporting evidence that a pattern of latitudinal variation exists. Male and female bonnetheads in north-west Florida also had the fastest growth rate compared with the other locations, supporting the hypothesis that growth rate is inversely related to the length of the growing season (i.e. a pattern of countergradient variation exists).
Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias
Authors: Landais I. , Ogliastro M. , Mita K. , Nohata J. , López-Ferber M. , Duonor-Cérutti M. , Shimada T. , Fournier P. , Devauchelle G.
Published: December 2003

Motivation: A whole set of Expressed Sequence Tags (ESTs) from the Sf9 cell line of Spodoptera frugiperda is presented here for the first time. By this way we want to identify both conserved and specific genes of this pest species. We also expect from this analysis to find a class of protein sequences providing a tool to explore genomic features and phylogeny of Lepidoptera.

Results: The ESTs display both housekeeping as well as developmentally regulated genes, and a high percentage of sequences with unknown function. Among the identified ORFs, almost all ribosomal proteins (RPs) were found with high EST redundancy and hence sequence accuracy. The codon usage found among RP genes is in average surprisingly much less biased in Lepidoptera than in other organisms. Other Spodoptera genes also displayed a low bias, suggesting a general genome expression feature in this Lepidoptera. We also found that the L35A and L36 RP sequences, respectively, display 40 and 10 amino-acid insertions, both being present only in insects. Sequence analysis suggests that they are probably not subjected to a strong selective pressure and may be good phylogenetic markers for Lepidoptera. Most interestingly, the Lepidoptera sequences of 9 RP genes displayed a specific signature different from the canonical one. We conclude that the RP family allows valuable comparative genomics and phylogeny of Lepidoptera.

Availability: All EST sequence data are available from the private ‘Spodo-Base’ upon request.
The MUSC DNA Microarray Database
Authors: Argraves Gary L. , Barth Jeremy L. , Argraves W. Scott
Published: December 2003

Summary: The Medical University of South Carolina (MUSC) DNA Microarray Database is a web-accessible archive of DNA microarray data. The database was developed using the DNA microarray project/data management system, μArrayDB. Annotations for each DNA microarray project and associated cRNA target information are stored in a MySQL relational database and linked to array hybridization data (raw and normalized). At the discretion of investigators, data are placed into the public domain where they can be interrogated and downloaded through a web browser. In addition to serving as an online resource of gene expression data, the MUSC DNA Microarray Database is a model for other academic DNA microarray data repositories.

Availability: Browsing and downloading of MUSC DNA Microarray Database information can be done after registration at http://proteogenomics.musc.edu/pss/home.php.
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences
Authors: Roset Roman , Subirana Juan A. , Messeguer Xavier
Published: December 2003

We have developed a program to determine the number, length and position of exact consecutive repeats of short sequences in DNA fragments or whole genomes. The program also gives the statistical significance of results by comparing them with those expected for a random sequence generated according to a Markovian model.

Availability: MREPATT can be accessed on line at http://www.lsi.upc.es/~alggen under the RESEARCH and SEARCH links.
Efficient estimation of emission probabilities in profile hidden Markov models
Authors: Ahola Virpi , Aittokallio Tero , Uusipaikka Esa , Vihinen Mauno
Published: December 2003

Motivation: Profile hidden Markov models provide a sensitive method for performing sequence database search and aligning multiple sequences. One of the drawbacks of the hidden Markov model is that the conserved amino acids are not emphasized, but signal and noise are treated equally. For this reason, the number of estimated emission parameters is often enormous. Focusing the analysis on conserved residues only should increase the accuracy of sequence database search.

Results: We address this issue with a new method for efficient emission probability (EEP) estimation, in which amino acids are divided into effective and ineffective residues at each conserved alignment position. A practical study with 20 protein families demonstrated that the EEP method is capable of detecting family members from other proteins with sensitivity of 98% and specificity of 99% on the average, even if the number of free emission parameters was decreased to 15% of the original. In the database search for TIM barrel sequences, EEP recognizes the family members nearly as accurately as HMMER or Blast, but the number of false positive sequences was significantly less than that obtained with the other methods.

Availability: The algorithms written in C language are available on request from the authors.
gff2aplot: Plotting sequence comparisons
Authors: Abril Josep F. , Guigó Roderic , Wiehe Thomas
Published: December 2003

Summary:  gff2aplot is a program to visualize the alignment of two sequences together with their annotations. Input for the program consists of single or multiple files in GFF-format which specify the alignment coordinates and annotation features of both sequences. Output is in PostScript format of any size. The features to be displayed are highly customizable to meet user specific needs. The program serves to generate print-quality images for comparative genome sequence analysis.

Availability:  gff2aplot is freely available under the GNU software licence and can be downloaded from the address specified below.

Supplementary information:  http://genome.imim.es/software/gfftools/GFF2APLOT.html
caCORE: A common infrastructure for cancer informatics
Authors: Covitz Peter A. , Hartel Frank , Schaefer Carl , De Coronado Sherri , Fragoso Gilberto , Sahni Himanso , Gustafson Scott , Buetow Kenneth H.
Published: December 2003

Motivation:Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications.

Results: We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP–XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources.

Availability: caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads.

Supplementary information:  http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).
MUTAGEN: Multi-User Tool for Annotating GENomes
Authors: Brügger Kim , Redder Peter , Skovgaard Marie
Published: December 2003

Summary: MUTAGEN is a free prokaryotic annotation system. It offers the advantages of genome comparison, graphical sequence browsers, search facilities and open-source for user-specific adjustments. The web-interface allows several users to access the system from standard desktop computers. The Sulfolobus acidocaldarius genome, and several plasmids and viruses have so far been analysed and annotated using MUTAGEN.

Availability: MUTAGEN is released as open-source software under GPL. The code is available for download and/or contribution at http://dac.molbio.ku.dk/bioinformatics/MUTAGEN/
GoFigure: Automated Gene Ontology™ annotation
Authors: Khan Salim , Situ Gang , Decker Keith , Schmidt Carl J.
Published: December 2003

Summary: We have developed a web tool to predict Gene Ontology (GO) terms. The tool accepts an input DNA or protein sequence, and uses BLAST to identify homologous sequences in GO annotated databases. A graph is returned to the user via email.

Availability: The tool is freely available at: http://udgenome.ags.udel.edu/frm_go.html/
SEMEDA: ontology based semantic integration of biological databases
Authors: Köhler Jacob , Philippi Stephan , Lange Matthias
Published: December 2003

Motivation: Many molecular biological databases are implemented on relational Database Management Systems, which provide standard interfaces like JDBC and ODBC for data and metadata exchange. By using these interfaces, many technical problems of database integration vanish and issues related to semantics remain, e.g. the use of different terms for the same things, different names for equivalent database attributes and missing links between relevant entries in different databases.

Results: In this publication, principles and methods that were used to implement SEMEDA (Semantic Meta Database) are described. Database owners can use SEMEDA to provide semantically integrated access to their databases as well as to collaboratively edit and maintain ontologies and controlled vocabularies. Biologists can use SEMEDA to query the integrated databases in real time without having to know the structure or any technical details of the underlying databases.

Availability: SEMEDA is available at http://www-bm.ipk-gatersleben.de/semeda/. Database providers who intend to grant access to their databases via SEMEDA are encouraged to contact the authors.
Metabolic pathways in three dimensions
Authors: Rojdestvenski Igor
Published: December 2003

Motivation: Currently a substantial research effort is devoted to automated representation of metabolic and gene networks. Automatic visualization plays a significant role in such efforts, and becomes an important problem on its own. Graphical visualization of metabolic pathways has to be information dense and not ‘overloaded’, recognizable and unified, close to traditional and algebraically consistent. The use of three-dimensional ‘virtual reality’ visualizations may help to understand better the intricate topology of metabolic and regulatory networks.

Results: A system of visualizing metabolic networks as graphs in three-dimensional space by means of Virtual Reality Modeling Language (VRML) is presented. The system is based on an XML-compliant MNV (‘Metabolic Network Visualizer’) language, and comprises MNV language standard and parser, MNV to VRML translator, and interactive pathway constructor, all unified by the HTML graphic user interface.

Availability: The MNV can be accessed in viewer mode at http://www.patronov.net/sciencevr/mnv/indexview.html or in constructor mode at http://www.patronov.net/sciencevr/mnv/indexmake.html

Supplementary information: The figures for the paper as well as the Appendices may be found at http://www.patronov.net/sciencevr/mnv/screenshots.html
Accelerating screening of 3D protein data with a graph theoretical approach
Authors: Frömmel Cornelius , Gille Christoph , Goede Andrean , Gröpl Clemens , Hougardy Stefan , Nierhoff Till , Preißner Robert , Thimm Martin
Published: December 2003

Motivation: The Dictionary of Interfaces in Proteins (DIP) is a database collecting the 3D structure of interacting parts of proteins that are called patches. It serves as a repository, in which patches similar to given query patches can be found. The computation of the similarity of two patches is time consuming and traversing the entire DIP requires some hours. In this work we address the question of how the patches similar to a given query can be identified by scanning only a small part of DIP. The answer to this question requires the investigation of the distribution of the similarity of patches.

Results: The score values describing the similarity of two patches can roughly be divided into three ranges that correspond to different levels of spatial similarity. Interestingly, the two iso-score lines separating the three classes can be determined by two different approaches. Applying a concept of the theory of random graphs reveals significant structural properties of the data in DIP. These can be used to accelerate scanning the DIP for patches similar to a given query. Searches for very similar patches could be accelerated by a factor of more than 25. Patches with a medium similarity could be found 10 times faster than by brute-force search.
PRIMEX: rapid identification of oligonucleotide matches in whole genomes
Authors: Lexa Matej , Valle Giorgio
Published: December 2003

Summary: PRIMEX (PRImer Match EXtractor) can detect oligonucleotide sequences in whole genomes, allowing for mismatches. Using a word lookup table and server functionality, PRIMEX accepts queries from client software and returns matches rapidly. We find it faster and more sensitive than currently available tools.

Availability: Running applications and source code have been made available at http://bioinformatics.cribi.unipd.it/primex
Using credibility intervals instead of hypothesis tests in SAGE analysis
Authors: Vêncio Ricardo Z.N. , Brentani Helena , Pereira Carlos A.B.
Published: December 2003

Motivation: Statistical methods usually used to perform Serial Analysis of Gene Expression (SAGE) analysis are based on hypothesis testing. They answer the biologist's question: ‘what are the genes with differential expression greater than r with P-value smaller than P?’. Another useful and not yet explored question is: ‘what is the uncertainty in differential expression ratio of a gene?’.

Results: We have used Bayesian model for SAGE differential gene expression ratios as a more informative alternative to hypothesis tests since it provides credibility intervals.

Availability: The model is implemented in R statistical language script and is available under GNU/GLP copyleft at supplemental web site.

Supplementary information:  http://www.ime.usp.br/~rvencio/SAGEci/
SPEPlip: the detection of signal peptide and lipoprotein cleavage sites
Authors: Fariselli Piero , Finocchiaro Giacomo , Casadio Rita
Published: December 2003

Summary: SPEPlip is a neural network-based method, trained and tested on a set of experimentally derived signal peptides from eukaryotes and prokaryotes. SPEPlip identifies the presence of sorting signals and predicts their cleavage sites. The accuracy in cross-validation is similar to that of other available programs: the rate of false positives is 4 and 6%, for prokaryotes and eukaryotes respectively and that of false negatives is 3% in both cases. When a set of 409 prokaryotic lipoproteins is predicted, SPEPlip predicts 97% of the chains in the signal peptide class. However, by integrating SPEPlip with a regular expression search utility based on the PROSITE pattern, we can successfully discriminate signal peptide-containing chains from lipoproteins. We propose the method for detecting and discriminating signal peptides containing chains and lipoproteins.

Availability: It can be accessed through the web page at http://gpcr.biocomp.unibo.it/predictors/
ModLoop: automated modeling of loops in protein structures
Authors: Fiser András , Sali Andrej
Published: December 2003

Summary: ModLoop is a web server for automated modeling of loops in protein structures. The input is the atomic coordinates of the protein structure in the Protein Data Bank format, and the specification of the starting and ending residues of one or more segments to be modeled, containing no more than 20 residues in total. The output is the coordinates of the non-hydrogen atoms in the modeled segments. A user provides the input to the server via a simple web interface, and receives the output by e-mail. The server relies on the loop modeling routine in MODELLER that predicts the loop conformations by satisfaction of spatial restraints, without relying on a database of known protein structures. For a rapid response, ModLoop runs on a cluster of Linux PC computers.

Availability: The server is freely accessible to academic users at http://salilab.org/modloop
Neutrophil Infiltration Increases Matrix Metalloproteinase-9 in the Ischemic Brain after Occlusion/Reperfusion of the Middle Cerebral Artery in Rats
Authors: Justicia Carles , Panés Julián , Solé Sónia , Cervera Álvaro , Deulofeu Ramon , Chamorro Ángel , Planas Anna M.
Published: December 2003

Matrix metalloproteinase-9 (MMP-9) activity increases in the brain during the first day after focal ischemia and might be involved in the pathogenesis of tissue damage. We previously showed MMP-9 in the extracellular space of brain parenchyma along with neutrophil recruitment after ischemia. In the present study, we tested whether neutrophils were a direct source of enhanced MMP-9 in the ischemic brain. Neutrophil infiltration was prevented either by injecting an antibody against ICAM-1, which abrogates neutrophil adhesion to the endothelial vessel wall, or by inducing neutropenia. One-hour intraluminal middle cerebral artery occlusion with reperfusion was induced, and studies were performed at 24 hours. Circulating neutrophils expressed 95-kDa MMP-9 and dimers, and infiltrated neutrophils stained positive for MMP-9. The expression of MMP-9 (mainly 95-kDa proform and dimers and, to a lesser extent, 88-kDa form) increased in brain after ischemia/reperfusion. Treatments preventing neutrophil infiltration failed to preclude the ischemia-induced increase in 88-kDa MMP-9 form and gelatinase activity in neurons and blood vessels. However, these treatments prevented the major increase in 95-kDa MMP-9 form and dimers. We conclude that neutrophil infiltration highly contributes to enhanced MMP-9 in the ischemic brain by releasing MMP-9 proform, which might participate in the tissular inflammatory reaction.
Determination of Volume of Distribution using Likelihood Estimation in Graphical Analysis: Elimination of Estimation Bias
Authors: Parsey Ramin V. , Ogden R. Todd , Mann J. John
Published: December 2003

The graphical analysis uses an ordinary least squares (OLS) fitting of transformed data to determine the total volume of distribution (VT) and is not dependent upon a compartmental model configuration. This method, however, suffers from a noise-dependent bias. Approaches for reducing this bias include incorporating a presmoothing step, minimizing the squared perpendicular distance to the regression line, and conducting multilinear analysis. The solution proposed by Ogden, likelihood estimation in graphical analysis (LEGA), is an estimation technique in the original (nontransformed) domain based upon standard likelihood theory that incorporates the specific assumptions made on the noise inherent in the measurements. To determine the impact of this new method upon the noise-dependent bias, we compared VT determinations by compartmental modeling, graphical analysis (GA), and LEGA in 36 regions of interest in dynamic PET data from 25 healthy volunteers injected with [11C]-WAY-100635 and [11C]-McN-5652, which are agents used to image the serotonin 1A receptor and serotonin transporter, respectively. As predicted by simulations, LEGA eliminates the noise-dependent bias associated with GA using OLS. This method is a valuable addition to the tools available for the quantification of radioligand binding data in PET and SPECT.
Screening for Down's syndrome in early and late first and second trimester using six maternal serum markers
Authors: Christiansen M , Larsen SO , Oxvig C , Qin Q‐P , Wagner JM , Overgaard MT , Gleich GJ , Sottrup‐Jensen L , Nørgaard‐Pedersen B
Published: December 2003

The efficiency of six maternal serum markers for Down's syndrome (DS), alpha fetoprotein (AFP), human chorionic gonadotropin (hCG), free β‐hCG, pregnancy‐associated plasma protein‐A (PAPP‐A), the proform of eosinophil major basic protein (ProMBP), pregnancy‐specific‐β‐1‐glycoprotein (SP1), and combinations thereof, was examined. Discriminant analysis in 156 DS pregnancies and 546 controls defined three effective combinations of serum marker logMoMs (multiples of the median in control samples) in three gestational age windows, i.e. Index I (weeks 7–9) = 0.52 logMoM ProMBP +  0.28 logMoM PAPP‐A − logMoM SP1; Index II (weeks 10–12) =  1.94 logMoM free β‐hCG − logMoM SP1, and Index III (weeks 15–19) =  0.78 logMoM free β‐hCG + 1.12 logMoM ProMBP − logMoM AFP. The estimated detection rates of indices and age for a false‐positive rate (FPR) of 5% were 73% for Index I, 69% for Index II, and 60% for Index III. Including the ultrasound marker nuchal translucency, using a DS at term risk of 1 : 400 as cut‐off, the detection rates of the indices increased to 86, 83, and 82% for FPRs of 4.3, 4.1, and 5.8%, respectively. The indices are promising markers for screening for DS.
Whaling or wailing?
Authors: Bridgewater Peter
Published: December 2003

On the face of it, international arguments about whaling are simple. There is broad support for the view that hunting whales should be banned, and strong opposition from certain countries. Yet the arguments are in fact much more complex, and illustrate among other things the growing gap between the existing legal framework and the issues it is now called upon to deal with. This gap in turn reflects the increasing complexity of environmental debate, and in particular the tensions between traditional conservationism and approaches hostile to anthropocentrism. The article emphasises how this framework encounters difficulties in dealing with human issues of cultural diversity as well as the “multi‐scale” nature of ecological dynamics. It concludes that, as debate has opened, the focus on urgent issues of conservation may have been lost.
Malocas and barracones. Tradition, biodiversity, and participation in the Colombian Amazon
Authors: Serje Margarita
Published: December 2003

This article offers an analysis of the assumptions and hypotheses that guide the resolve of an NGO in the Colombian Amazon to strengthen indigenous autonomy and the traditional forms of environmental management, thereby seeking to guarantee preservation of the region's biodiversity. An examination of the practices stemming from these postulates reveals the paradox of the action of projects and programmes which, in their eagerness to put traditional knowledge first, end up as the purveyors of rational epistemology and logic. This process is shown through reference to the uses made throughout history of the maloca, the traditional indigenous dwelling of north‐west Amazonia, and of the barracón, an edifice introduced with the commercial exploitation of rubber, a paradigm of the “unbridled capitalism” that has spearheaded the violent colonisation of the region.
Social sciences and biodiversity – connections between the global and the local in Viet Nam
Authors: Hiêu Dinh Trong
Published: December 2003

The NGOs working in Viet Nam in the field of biodiversity often cooperate with local researchers in the natural sciences, which is understandable. But they often overlook researchers in the social sciences, or have recourse to their expertise only in the case of feasibility studies. Conversely, social science research conducted by the Vietnamese often neglects the natural science aspects. This article sets out to show that these are indeed local institutions whose preoccupations match the global concern for preserving biodiversity, but that there is also a need to stimulate basic research aimed at determining more precisely, from a historical standpoint in particular, how the Vietnamese concept of nature has evolved.
Local knowledge in the hands of transnational NGO networks: a Mexican viewpoint*
Authors: Dumoulin David
Published: December 2003

Transnational environmental NGOs (ENGOs) have played a leading role in furthering the cause of local knowledge of biodiversity, and indeed of most environmental issues, in national and international arenas. But it is impossible to present this as a unified drive, because the generic term “NGO” is now virtually meaningless. Focusing on the international roles and the internal workings of ENGOs, this article sets out to show how there have been three main blocs of actors since 1990: the epistemic community striving to safeguard cultural and biological diversity, the globalised nature reserves sector and the transnational advocacy networks. The fact that the local knowledge issue has entered international arenas through debate on the global environmental crisis is the key to understanding such knowledge. Furthermore, that understanding of “local” knowledge hinges on insight into the thinking behind the actions and the political stance of each of those three blocs of actors. Examining the interconnection between the international and the national – in this case, Mexican – contexts reveals how local knowledge has become an important issue‐area, with significant political implications.
US environmental NGOs and the Cree. An unnatural alliance for the preservation of nature?
Authors: Roué Marie
Published: December 2003

This article will attempt to understand the complex relations between indigenous peoples and environmental NGOs in the context of conflict caused by a hydroelectric development mega‐project in James Bay in subarctic Quebec. There is an ambiguity in the mediator and spokesperson role that NGOs take on in defending the cause of indigenous peoples, in so far as they oscillate between acting as mere middlemen, as brokers, and as patrons. Even beyond the tangle of multiple and conflicting interests, however, environmentalists are torn between their own conceptions of nature and those of the people they defend. Environmentalists are heirs to the notion, characteristic of the pioneers who discovered America through the prism of the Bible: a wild and threatening “wilderness”, to this, they have now added the objective of protecting nature against threats posed by humans. In both conceptions, which have successively haunted Western imaginations, nature offers to humans, when lost in its vastness and far from their fellows, a direct relation alongside God. How then might it be possible to work with the Cree, and indigenous peoples generally, to protect a nature that they do not regard as separate from humankind, but of which they are an integral part? How long will it remain possible to do without an analysis of the concept of nature conservation which, in the context of shared environmental causes, establishes our relation to others even as we exclude them?
NGOs and the process of prior informed consent in bioprospecting research: the Maya ICBG project in Chiapas, Mexico
Authors: Berlin Brent , Ann Berlin Elois
Published: December 2003

In 1998, a 5‐year bioprospecting project that came to be known as the Maya ICBG was initiated among the Maya communities of the Highlands of Chiapas, Mexico. The project was funded by agencies of the US government – the National Institutes of Health, the National Science Foundation, and the US Department of Agriculture. Project personnel were drawn from a major US university, a federal Mexican research institution, a small British pharmaceutical company, and numerous Maya collaborators. The major aims of the research included drug discovery and pharmaceutical development, medical ethnobiology and floristic inventory, and conservation, sustained harvest, and economic growth. In spite of strong support from local Maya communities and Mexican federal agencies, the project was terminated in its second year due to the actions of local, national, and international non‐governmental organisations, which characterised the project as biopiracy. Major themes in the acrimonious debate that developed concerned the definition of prior informed consent (PIC), local communities' rights to grant PIC, and who should judge whether PIC had been obtained. In this paper, we describe the events leading to the termination of the Maya ICBG and question the motives and methods of certain NGOs in usurping the rights of local communities to act on their own behalf concerning the sustainable use of their own biological resources.
The Function of the Post‐Nominal Element ki∼k'un in Lakota
Authors: Ingham Bruce
Published: December 2003

The Lakota post‐nominal element ki∼k'un lends itself to analysis as either a definite article or a topic marker. It can occur more than once in a sentence, though there are special conditions for this, but it does not occur with all notionally definite items, especially when associated with a postposition. Also it has the further function of relative clause marker and general subordinator. Comparison of texts shows that in narratives and non analytical texts it occurs less frequently per sentence, thus supporting the topic marker analysis, while in analytic discourse it occurs more frequently, supporting the definite article analysis.
Identification of differentially expressed genes in models of melanoma progression by cDNA array analysis: SPARC, MIF and a novel cathepsin protease characterize aggressive phenotypes
Authors: Rumpler G. , Becker B. , Hafner C. , McClelland M. , Stolz W. , Landthaler M. , Schmitt R. , Bosserhoff A. , Vogt T.
Published: December 2003

Abstract:  Currently, the scale and consistency of changes of gene expression profiles in models of melanoma progression are largely unknown. Therefore, we investigated siblings of cell lines of malignant melanomas (MM), which have been selected by nude mouse passages for (a) increased tumorigenicity (local ECM‐independent growth), (b) metastatic potential, or (c) selected for increased invasiveness using the Boyden chamber. cDNA array analysis surveying more than 27.000 transcripts per cell line showed that 1.5–2.8% of all detectable transcripts were consistently differentially regulated during the selection processes in those models. Using array analysis, we identified 33 individual transcripts that exhibited significant differential hybridization paralleling the increased aggressiveness of the selected progeny. Because some of those genes could play a significant functional role in the progression of MM, we additionally proved their regulative pattern using Northern blotting. Among others, progressive overexpression of osteonectin/SPARC, a molecule that is known to be involved in tissue remodeling and angiogenesis, was found in the selected offspring from all three experimental models and may therefore be considered as a potential marker for aggressive MM as well as a promising therapeutic target. We further show that the selection of MM cells for increased ECM‐independent local growth was accompanied by overexpression of macrophage migration inhibiting factor (MIF), an important modulator of both cell cycle progression and angiogenesis, and cathepsin Z, a novel member of the family of matrix degrading proteinases.
Histological evaluation of the effects of angiotensin peptides on wound repair in diabetic mice
Authors: Rodgers Kathleen E. , Roda Norma , Felix Juan C. , Espinoza Theresa , Maldonado Sonia , DiZerega Gere
Published: December 2003

Abstract:  Recent studies have shown that angiotensin peptides accelerate dermal repair. Histological observation of samples taken at the termination of studies showed that the wounds treated with peptides were more mature and organized by day 25 after full thickness excision in diabetic mice. However, the mechanism by which this acceleration occurs has not been determined. In the experiments described here, the effect of angiotensin peptides [AII, A(1–7) and NorLeu3‐A(1–7)] on the quality of the healing wound was evaluated histologically. Administration of the peptides accelerated collagen deposition, re‐epithelialization and new blood vessel formation. By day 4, the percentage of the wound with collagen increased two‐ to six‐fold depending upon the peptide. The increase by angiotensin peptides continued throughout the experimental period. On days 4 and 7 (only) after injury, exposure to angiotensin peptides increased the number of blood vessels at the wound site two‐ to three‐fold. Finally, the percentage of the wound site covered with new epithelium increased after administration of angiotensin peptides. Re‐epithelialization was observed as early as day 4 in wounds treated with angiotensin peptides. The increase was greater at later time points [up to 8‐fold at day 14 with NorLeu3‐A(1–7)]. Fibroblast infiltration and proliferation occurred earlier in wounds treated with angiotensin peptides. Wounds treated with A(1–7) and NorLeu3‐A(1–7) had an increase in neutrophils and macrophages on day 4 after wounding. Overall, administration of these peptides resulted in a healing site that was more mature, including reorganization of the collagen into a basket‐weave appearance. Further, these studies confirm the superiority of NorLeu3‐A(1–7) to AII and A(1–7) in wound healing evaluated at a microscopic level.
Evaluation of combined gene regulatory elements for transcriptional targeting of suicide gene expression to malignant melanoma
Authors: Rothfels Heike , Paschen Annette , Schadendorf Dirk
Published: December 2003

Abstract:  Selective killing of tumors can be achieved by targeting the transcription of suicide genes via specific DNA control elements to malignant cells. Three different enhancer‐promoter systems were constructed and evaluated for their capability to direct gene expression to melanoma. Two tissue‐specific (tyrosinase and MIA) promoters and one weak viral promoter were fused to multiple tandem copies of a melanocyte‐specific enhancer element. Reporter gene assays revealed a maximum increase in transcription by combining each promoter with 3–4 copies of the enhancer and demonstrated that all enhancer‐promoter combinations exhibited tissue‐specific activity. Though this activity was still significantly less than that of the strong but unspecific cytomegalo virus (CMV) promoter. In contrast, when these combinations were employed to drive the expression of two suicide genes, encoding the diphtheria toxin A chain (DT‐A) and the prodrug‐activating herpes simplex virus thymidine kinase (TK), respectively, only those constructs in which transcription was under the control of tissue‐specific promoter elements mediated selective killing of melanoma cells. This killing was in the range of cell death induced by CMV promoter activity. Our data indicate that the enhancer/tyrosinase and enhancer/MIA promoter constructs but not the viral promoter constructs can provide a valuable tool for selective suicide gene expression in melanoma.
hMLH1 and hMSH2 gene mutations are present in radial growth‐phase cutaneous malignant melanoma cell lines and can be induced further by ultraviolet‐B irradiation
Authors: Hussein Mahmoud R. , Wood Gary S.
Published: December 2003

Abstract: Microsatellite instability and reduced expression of mismatch repair proteins were reported in melanomas. However, little is known about the mutational changes of the mismatch repair genes in radial growth‐phase melanoma especially following UVB irradiation. To investigate these changes, an in vitro system consisting of radial growth‐phase Wistar melanoma cell lines (WM35, WM3211 and WM1650) was established. The cells were UVB irradiated (10 mJ/cm2), and evaluated for mutational changes of exon regions 13, 16 and 19 (hMLH1) and 6, 7 and 12 (hMSH2) of these genes before and after irradiation. The genomic DNAs were PCR amplified and the products were directly sequenced. Transition (C→T, G→A, T→C) and transversion (G→T, A→T) mutations were found in exons 6, 16 and 19. Some were present in both the sham‐irradiated and UV‐irradiated cells but others were only detected after UVB irradiation. hMLH1 and hMSH2 gene mutations occur early in melanoma tumorigenesis. The ability of UVB irradiation to induce additional mutations in these repair genes suggests its possible role in melanoma pathogenesis. Further investigation will be needed to determine whether mutations such as these contribute to the development of microsatellite instability in melanoma.
Purinergic receptor expression in the regenerating epidermis in a rat model of normal and delayed wound healing
Authors: Greig Aina V. H. , James Stuart E. , McGrouther D Angus , Terenghi Giorgio , Burnstock Geoffrey
Published: December 2003

Abstract:  This study investigated changes in the protein expression of purinergic receptors in the regenerating rat epidermis during normal wound healing, in denervated wounds, and in denervated wounds treated with nerve growth factor (NGF), where wound healing rates are normalized. Excisional wounds were placed within denervated, pedicled, oblique, groin skin flaps, and in the contralateral abdomen to act as a control site. Six rats had NGF‐treated wounds and six had untreated wounds. Tissue was harvested at day four after wounding. The re‐epithelializing wound edges were analyzed immunohistochemically for P2X5, P2X7, P2Y1 and P2Y2 receptors, and immunostaining of keratinocytes was quantified using optical densitometry.

In normal rat epidermis, P2Y1 and P2Y2 receptors were found in the basal layer where keratinocytes proliferate; P2X5 receptors were associated with proliferating and differentiating epidermal keratinocytes in basal and suprabasal layers; P2X7 receptors were associated with terminally differentiated keratinocytes in the stratum corneum. In the regenerating epidermis of denervated wounds, P2Y1 receptor protein expression was significantly increased in keratinocytes (P < 0.001) but P2Y2 receptor protein expression was significantly decreased (P < 0.001). Conversely, NGF treatment of denervated wounds, reduced expression of P2Y1 receptors (P < 0.001) in keratinocytes but enhanced expression of the P2Y2 receptors (P < 0.01) compared with untreated denervated wounds. In innervated wounds, NGF treatment enhanced P2X5 (P < 0.001) and P2Y1 receptor protein (P < 0.001) expression in keratinocytes. P2X7 receptors were absent in all experimental wound healing preparations. P2X5, P2X7, P2Y1 and P2Y2 receptor protein expression in the regenerating epidermis was altered both during wound healing and also by NGF treatment. Possible roles for purinergic signalling and its relation to NGF in wound healing are discussed.