bluuebunny/crossref_metadata_2025 huggingface dataset:
Groundwater flow, heat transport, and water table position within volcanic edifices: Implications for volcanic processes in the Cascade Range
Authors: Hurwitz Shaul , Kipp Kenneth L. , Ingebritsen Steven E. , Reid Mark E.
Published: December 2003

The position of the water table within a volcanic edifice has significant implications for volcano hazards, geothermal energy, and epithermal mineralization. We have modified the HYDROTHERM numerical simulator to allow for a free‐surface (water table) upper boundary condition and a wide range of recharge rates, heat input rates, and thermodynamic conditions representative of continental volcano‐hydrothermal systems. An extensive set of simulations was performed on a hypothetical stratovolcano system with unconfined groundwater flow. Simulation results suggest that the permeability structure of the volcanic edifice and underlying material is the dominant control on water table elevation and the distribution of pressures, temperatures, and fluid phases at depth. When permeabilities are isotropic, water table elevation decreases with increasing heat flux and increases with increasing recharge, but when permeabilities are anisotropic, these effects can be much less pronounced. Several conditions facilitate the ascent of a hydrothermal plume into a volcanic edifice: a sufficient source of heat and magmatic volatiles at depth, strong buoyancy forces, and a relatively weak topography‐driven flow system. Further, the plume must be connected to a deep heat source through a pathway with a time‐averaged effective permeability ≥1 × 10−16 m2, which may be maintained by frequent seismicity. Topography‐driven flow may be retarded by low permeability in the edifice and/or the lack of precipitation recharge; in the latter case, the water table may be relatively deep. Simulation results were compared with observations from the Quaternary stratovolcanoes along the Cascade Range of the western United States to infer hydrothermal processes within the edifices. Extensive ice caps on many Cascade Range stratovolcanoes may restrict recharge on the summits and uppermost flanks. Both the simulation results and limited observational data allow for the possibility that the water table beneath the stratovolcanoes is relatively deep.
Multiple effects of mefenamic acid on K+ currents in smooth muscle cells from pig proximal urethra
Authors: Teramoto N , Brading A F , Ito Y
Published: December 2003

The effects of mefenamic acid on both membrane potential and K+ currents in pig urethral myocytes were investigated using patch‐clamp techniques (conventional whole‐cell, cell‐attached, outside‐out and inside‐out configuration).

In the current‐clamp mode, mefenamic acid caused a concentration‐dependent hyperpolarization, which was inhibited by preapplication of 1 μM glibenclamide. In the voltage‐clamp mode, mefenamic acid induced an outward current that was blocked by glibenclamide even in the presence of iberiotoxin (IbTX, 300 nM) at −50 mV.

ATP‐sensitive K+ channels (KATP channels) could be activated in the same patch by mefenamic acid and levcromakalim, with the same unitary amplitude and the similar opening gating at −50 mV in cell‐attached configuration.

In outside‐out recording, external application of mefenamic acid activated intracellular Ca2+‐activated IbTX‐sensitive large‐conductance K+ channels (BKCa channels).

Mefenamic acid (30 μM) activated spontaneous transient outward currents (STOCs). In contrast, mefenamic acid (100 μM) increased sustained outward currents, diminishing the activity of STOCs.

Over the whole voltage range, mefenamic acid caused opposite effects on the membrane currents in the absence and presence of 5 μM glibenclamide. In the presence of 10 mM 4‐aminopyridine (4‐AP), mefenamic acid only increased the outward currents.

These results indicate that mefenamic acid increases the channel activities of two distinct types of K+ channels (i.e. BKCa channels and KATP channels) and decreased 4‐AP‐sensitive K+ channels in pig urethral myocytes.

British Journal of Pharmacology (2003) 140, 1341–1350. doi:10.1038/sj.bjp.0705524
Thymol, a constituent of thyme essential oil, is a positive allosteric modulator of human GABAA receptors and a homo‐oligomeric GABA receptor from Drosophila melanogaster
Authors: Priestley Caroline M , Williamson Elizabeth M , Wafford Keith A , Sattelle David B
Published: December 2003

The GABA‐modulating and GABA‐mimetic activities of the monoterpenoid thymol were explored on human GABAA and Drosophila melanogaster homomeric RDLac GABA receptors expressed in Xenopus laevis oocytes, voltage‐clamped at −60 mV. The site of action of thymol was also investigated.

Thymol, 1–100 μM, resulted in a dose‐dependent potentiation of the EC20 GABA response in oocytes injected with either α1β3γ2s GABAA subunit cDNAs or the RDLac subunit RNA. At 100 μM thymol, current amplitudes in response to GABA were 416±72 and 715±85% of controls, respectively. On both receptors, thymol, 100 μM, elicited small currents in the absence of GABA.

The EC50 for GABA at α1β3γ2s GABAA receptors was reduced by 50 μM thymol from 15±3 to 4±1 μM, and the Hill slope changed from 1.35±0.14 to 1.04±0.16; there was little effect on the maximum GABA response.

Thymol (1–100 μM) potentiation of responses to EC20 GABA for α1β1γ2s, α6β3γ2s and α1β3γ2s human GABAA receptors was almost identical, arguing against actions at benzodiazepine or loreclezole sites.

Neither flumazenil, 3‐hydroxymethyl‐β‐carboline (3‐HMC), nor 5α‐pregnane‐3α, 20α‐diol (5α‐pregnanediol) affected thymol potentiation of the GABA response at α1β3γ2s receptors, providing evidence against actions at the benzodiazepine/β‐carboline or steroid sites. Thymol stimulated the agonist actions of pentobarbital and propofol on α1β3γ2s receptors, consistent with a mode of action distinct from that of either compound. These data suggest that thymol potentiates GABAA receptors through a previously unidentified binding site.

British Journal of Pharmacology (2003) 140, 1363–1372. doi:10.1038/sj.bjp.0705542
Presynaptic group I metabotropic glutamate receptors modulate synaptic transmission in the rat superior colliculus via 4‐AP sensitive K+ channels
Authors: White Anne‐Marie , Kylänpää Risto A , Christie Louisa A , McIntosh Simon J , Irving Andrew J , Platt Bettina
Published: December 2003

Group I metabotropic glutamate receptors (mGluRs) are thought to be important modulators of neuronal function in the superior colliculus (SC). Here, we investigated the pharmacology and signalling mechanisms underlying group I mGluR‐mediated inhibition of neuronal excitability and synaptic transmission in the rat SC slice.

The group I agonist (RS)‐3,5‐dihydroxyphenylglycine (DHPG) potently depressed synaptically evoked excitatory postsynaptic potentials (EPSPs), currents (EPSCs), and action potentials in a dose‐dependent manner (IC50: 6.3 μM). This was strongly reduced by the broad‐spectrum antagonist (+)‐alpha‐methyl‐4‐carboxyphenylglycine (MCPG, 1 mM, ∼95% reduction), by the mGluR1 antagonist LY367385 (100 μM, ∼80% reduction) but not by the mGluR5 antagonist 6‐methyl‐2‐(phenylethynyl)‐pyridine (MPEP, 1–100 μM).

The putative mGluR5‐specific agonist (RS)‐2‐chloro‐5‐hydroxyphenylglycine (CHPG, 500 μM) also inhibited EPSPs. Interestingly, CHPG's actions were not blocked by MPEP, but LY367385 (100 μM) reduced the effect of CHPG by 50%.

Inhibition induced by DHPG was independent of phospholipase C (PLC)/protein kinase C pathways, and did not require intact intracellular Ca2+ stores. It was not abolished but enhanced by the GABAA antagonist bicuculline (5 μM), suggesting that DHPG's action was not due to facilitated inhibition or changes in neuronal network activity.

The K+ channel antagonist 4‐aminopyridine (4‐AP, 50–100 μM) converted the inhibitory effect of DHPG into facilitation. Paired‐pulse depression was strongly reduced by DHPG, an effect that was also prevented by 4‐AP.

Our data indicate that group I agonists regulate transmitter release, presumably via an autoreceptor in the SC. This receptor may be involved in adaptation to repetitive stimulation via a non‐PLC mediated pathway.

British Journal of Pharmacology (2003) 140, 1421–1433. doi:10.1038/sj.bjp.0705570
The Cl− channel blocker niflumic acid releases Ca2+ from an intracellular store in rat pulmonary artery smooth muscle cells
Authors: Cruickshank Stuart F , Baxter Lynne M , Drummond Robert M
Published: December 2003

The effect of the Cl− channel blockers niflumic acid (NFA), 5‐nitro‐2‐(3‐phenylpropylamino)‐benzoic acid (NPPB), 4,4′‐diisothiocyanatostilbene‐2,2′‐disulfonic acid (DIDS), and anthracene‐9‐carboxylic acid (A‐9‐C), on Ca2+ signalling in rat pulmonary artery smooth muscle cells was examined. Intracellular Ca2+ concentration ([Ca2+]i) was monitored with either fura‐2 or fluo‐4, and caffeine was used to activate the ryanodine receptor, thereby releasing Ca2+ from the sarcoplasmic reticulum (SR).

NFA and NPPB significantly increased basal [Ca2+]i and attenuated the caffeine‐induced increase in [Ca2+]i. These Cl− channel blockers also increased the half‐time (t1/2) to peak for the caffeine‐induced [Ca2+]i transient, and slowed the removal of Ca2+ from the cytosol following application of caffeine. Since DIDS and A‐9‐C were found to adversely affect fura‐2 fluorescence, fluo‐4 was used to monitor intracellular Ca2+ in studies involving these Cl− channel blockers. Both DIDS and A‐9‐C increased basal fluo‐4 fluorescence, indicating an increase in intracellular Ca2+, and while DIDS had no significant effect on the t1/2 to peak for the caffeine‐induced Ca2+ transient, it was significantly increased by A‐9‐C.

In the absence of extracellular Ca2+, NFA significantly increased basal [Ca2+]i, suggesting that the release of Ca2+ from an intracellular store was responsible for the observed effect.

Depleting the SR with the combination of caffeine and cyclopiazonic acid prevented the increase in basal [Ca2+]i induced by NFA. Additionally, incubating the cells with ryanodine also prevented the increase in basal [Ca2+]i induced by NFA.

These data show that Cl− channel blockers have marked effects on Ca2+ signalling in pulmonary artery smooth muscle cells. Furthermore, examination of the NFA‐induced increase in [Ca2+]i indicates that it is likely due to Ca2+ release from an intracellular store, most probably the SR.

British Journal of Pharmacology (2003) 140, 1442–1450. doi:10.1038/sj.bjp.0705571
An optimized approach to study endocannabinoid signaling: evidence against constitutive activity of rat brain adenosine A1 and cannabinoid CB1 receptors
Authors: Savinainen Juha R , Saario Susanna M , Niemi Riku , Järvinen Tomi , Laitinen Jarmo T
Published: December 2003

At nanomolar concentrations, SR141716 and AM251 act as specific and selective antagonists of the cannabinoid CB1 receptor. In the micromolar range, these compounds were shown to inhibit basal G‐protein activity, and this is often interpreted to implicate constitutive activity of the CB1 receptors in native tissue. We show here, using [35S]GTPγS binding techniques, that micromolar concentrations of SR141716 and AM251 inhibit basal G‐protein activity in rat cerebellar membranes, but only in conditions where tonic adenosine A1 receptor signaling is not eliminated.

Unlike lipophilic A1 receptor antagonists (potency order DPCPX≫N‐0840 ∼cirsimarin>caffeine), adenosine deaminase (ADA) was not fully capable in eliminating basal A1 receptor‐dependent G‐protein activity. Importantly, all antagonists reduced basal signal to the same extent (20%), and the response evoked by the inverse agonist DPCPX was not reversed by the neutral antagonist N‐0840. These data indicate that rat brain A1 receptors are not constitutively active, but that an ADA‐resistant adenosine pool is responsible for tonic A1 receptor activity in brain membranes.

SR141716 and AM251, at concentrations fully effective in reversing CB1‐mediated responses (10−6 M), did not reduce basal G‐protein activity, indicating that CB1 receptors are not constitutively active in these preparations.

At higher concentrations (1–2.5 × 10−5 M), both antagonists reduced basal G‐protein activity in control and ADA‐treated membranes, but had no effect when A1 receptor signaling was blocked with DPCPX. Moreover, the CB1 antagonists right‐shifted A1 agonist dose–response curves without affecting maximal responses, suggesting competitive mode of antagonist action. The CB1 antagonists did not affect muscarinic acetylcholine or GABAB receptor signaling.

When further optimizing G‐protein activation assay for the labile endocannabinoid 2‐arachidonoylglycerol (2‐AG), we show, by using HPLC, that pretreatment of cerebellar membranes with methyl arachidonoyl fluorophosphonate (MAFP) fully prevented enzymatic degradation of 2‐AG and concomitantly enhanced the potency of 2‐AG. In contrast to previous claims, MAFP exhibited no antagonist activity at the CB1 receptor.

The findings establish an optimized method with improved signal‐to‐noise ratio to assess endocannabinoid‐dependent G‐protein activity in brain membranes, under assay conditions where basal adenosinergic tone and enzymatic degradation of 2‐AG are fully eliminated.

British Journal of Pharmacology (2003) 140, 1451–1459. doi:10.1038/sj.bjp.0705577
Effect of peptidases on the ability of exogenous and endogenous neurokinins to produce neurokinin 1 receptor internalization in the rat spinal cord
Authors: Marvizón Juan Carlos G , Wang Xueren , Lao Li‐Jun , Song Bingbing
Published: December 2003

The ability of peptidases to restrict neurokinin 1 receptor (NK1R) activation by exogenously applied or endogenously released neurokinins was investigated by measuring NK1R internalization in rat spinal cord slices.

Concentration–response curves for substance P and neurokinin A were obtained in the presence and absence of 10 μM thiorphan, an inhibitor of neutral endopeptidase (EC 3.4.24.11), plus 10 μM captopril, an inhibitor of dipeptidyl carboxypeptidase (EC 3.4.15.1). These inhibitors significantly decreased the EC50 of substance P to produce NK1R internalization from 32 to 9 nM, and the EC50 of neurokinin A from 170 to 60 nM.

Substance P was significantly more potent than neurokinin A, both with and without these peptidase inhibitors.

In the presence of peptidase inhibitors, neurokinin B was 10 times less potent than neurokinin A and 64 times less potent than substance P (EC50=573 nM).

Several aminopeptidase inhibitors (actinonin, amastatin, bacitracin, bestatin and puromycin) failed to further increase the effect of thiorphan plus captopril on the NK1R internalization produced by 10 nM substance P.

Electrical stimulation of the dorsal root produced NK1R internalization by releasing endogenous neurokinins. Thiorphan plus captopril increased NK1R internalization produced by 1 Hz stimulation, but not by 30 Hz stimulation.

Therefore, NEN and DCP restrict NK1R activation by endogenous neurokinins when they are gradually released by low‐frequency firing of primary afferents, but become saturated or inhibited when primary afferents fire at a high frequency.

British Journal of Pharmacology (2003) 140, 1389–1398. doi:10.1038/sj.bjp.0705578
Linkage and QTL mapping for Sus scrofa chromosome 13
Authors: Yue G. , Russo V. , Davoli R. , Sternstein I. , Brunsch C. , Schröffelova D. , Stratil A. , Moser G. , Bartenschlager H. , Reiner G. , Geldermann H.
Published: December 2003

For Sus scrofa chromosome 13 (SSC13) eleven markers were genotyped to generate linkage and QTL maps in three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. Results of linkage maps were similar and agreed with published maps. Quantitative trait loci (QTLs) for body weights, meat conductivity and fat deposition were mapped in the M × P family to the interval S0076–S0068 (40–80 cM) and near the locus SW38 (120–150 cM). QTLs for the same traits were observed in the W × M family in different intervals explaining up to 5.3% of the F2 phenotypic variance. No significant QTLs for the traits under investigation were found in the W × P family. The effects of QTL alleles were mostly dominant. In the M × P and W × M families alleles inherited from Meishan were generally associated with high values of live weights, food consumption and fat deposition and low values of meat conductivity.
Effects of environmental variation on extinction and establishment
Authors: Drake John M. , Lodge David M.
Published: December 2003

Theoretical models predict that increasing environmental variation increases the probability of extinction, decreases the probability of establishment, and influences the distribution of times to extinction or establishment. We conducted an experiment with 281 independent populations of Daphnia magna under controlled laboratory conditions to test these predictions. Consistent with the theory, the fraction of populations going extinct increased and the fraction of populations establishing self‐sustaining populations decreased under higher levels of environmental variation compared with controls. Time to extinction decreased under higher levels of environmental variation, but we found no effect on time to establishment. These results are consistent with theoretical predictions from models of extinction. They therefore support the use of stochastic population models to predict the fates of introductions of non‐indigenous species or native endangered species based on historic fluctuations and/or expected future conditions.
Power‐law species–area relationships and self‐similar species distributions within finite areas
Authors: Šizling Arnošt L. , Storch David
Published: December 2003

The species–area relationship (SAR) is often expressed as a power law, which indicates scale invariance. It has been claimed that the scale invariance – or self‐similarity at the community level – is not compatible with the self‐similarity at the level of spatial distribution of individual species, because the power law would only emerge if distributions for all species had identical fractal dimensions (FD). Here we show that even if species differ in their FD, the resulting SAR is approximately linear on a log–log scale because observed spatial distributions are inevitably spatially restricted – a phenomenon we term the ‘finite‐area effect’. Using distribution atlases, we demonstrate that the apparent power law of SARs for central European birds is attributable to this finite‐area effect affecting species that indeed reveal self‐similar distributions. We discuss implications of this mechanism producing the SAR.
Measurement error and estimates of population extinction risk
Authors: McNamara John M. , Harding Karin C.
Published: December 2003

It is common to estimate the extinction probability for a vulnerable population using methods that are based on the mean and variance of the long‐term population growth rate. The numerical values of these two parameters are estimated from time series of population censuses. However, the proportion of a population that is registered at each census is typically not constant but will vary among years because of stochastic factors such as weather conditions at the time of sampling. Here, we analyse how such sampling errors influence estimates of extinction risk and find sampling errors to produce two opposite effects. Measurement errors lead to an exaggerated overall variance, but also introduce negative autocorrelations in the time series (which means that estimates of annual growth rates tend to alternate in size). If time series data are treated properly these two effects exactly counter balance. We advocate routinely incorporating a measure of among year correlations in estimating population extinction risk.
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
Authors: Wang Ting , Stormo Gary D.
Published: December 2003

Motivation: Discovery of regulatory motifs in unaligned DNA sequences remains a fundamental problem in computational biology. Two categories of algorithms have been developed to identify common motifs from a set of DNA sequences. The first can be called a ‘multiple genes, single species’ approach. It proposes that a degenerate motif is embedded in some or all of the otherwise unrelated input sequences and tries to describe a consensus motif and identify its occurrences. It is often used for co-regulated genes identified through experimental approaches. The second approach can be called ‘single gene, multiple species’. It requires orthologous input sequences and tries to identify unusually well conserved regions by phylogenetic footprinting. Both approaches perform well, but each has some limitations. It is tempting to combine the knowledge of co-regulation among different genes and conservation among orthologous genes to improve our ability to identify motifs.

Results: Based on the Consensus algorithm previously established by our group, we introduce a new algorithm called PhyloCon (Phylogenetic Consensus) that takes into account both conservation among orthologous genes and co-regulation of genes within a species. This algorithm first aligns conserved regions of orthologous sequences into multiple sequence alignments, or profiles, then compares profiles representing non-orthologous sequences. Motifs emerge as common regions in these profiles. Here we present a novel statistic to compare profiles of DNA sequences and a greedy approach to search for common subprofiles. We demonstrate that PhyloCon performs well on both synthetic and biological data.

Availability: Software available upon request from the authors. http://ural.wustl.edu/softwares.html
Scoring clustering solutions by their biological relevance
Authors: Gat-Viks I. , Sharan R. , Shamir R.
Published: December 2003

Motivation: A central step in the analysis of gene expression data is the identification of groups of genes that exhibit similar expression patterns. Clustering gene expression data into homogeneous groups was shown to be instrumental in functional annotation, tissue classification, regulatory motif identification, and other applications. Although there is a rich literature on clustering algorithms for gene expression analysis, very few works addressed the systematic comparison and evaluation of clustering results. Typically, different clustering algorithms yield different clustering solutions on the same data, and there is no agreed upon guideline for choosing among them.

Results: We developed a novel statistically based method for assessing a clustering solution according to prior biological knowledge. Our method can be used to compare different clustering solutions or to optimize the parameters of a clustering algorithm. The method is based on projecting vectors of biological attributes of the clustered elements onto the real line, such that the ratio of between-groups and within-group variance estimators is maximized. The projected data are then scored using a non-parametric analysis of variance test, and the score's confidence is evaluated. We validate our approach using simulated data and show that our scoring method outperforms several extant methods, including the separation to homogeneity ratio and the silhouette measure. We apply our method to evaluate results of several clustering methods on yeast cell-cycle gene expression data.

Availability: The software is available from the authors upon request.
Classification of protein quaternary structure with support vector machine
Authors: Zhang Shao-Wu , Pan Quan , Zhang Hong-Cai , Zhang Yun-Long , Wang Hai-Yu
Published: December 2003

Motivation: Since the gap between sharply increasing known sequences and slow accumulation of known structures is becoming large, an automatic classification process based on the primary sequences and known three-dimensional structure becomes indispensable. The classification of protein quaternary structure based on the primary sequences can provide some useful information for the biologists. So a fully automatic and reliable classification system is needed. This work tries to look for the effective methods of extracting attribute and the algorithm for classifying the quaternary structure from the primary sequences.

Results: Both of the support vector machine (SVM) and the covariant discriminant algorithms have been first introduced to predict quaternary structure properties from the protein primary sequences. The amino acid composition and the auto-correlation functions based on the amino acid index profile of the primary sequence have been taken into account in the algorithms. We have analyzed 472 amino acid indices and selected the four amino acid indices as the examples, which have the best performance. Thus the five attribute parameter data sets (COMP, FASG, NISK, WOLS and KYTJ) were established from the protein primary sequences. The COMP attribute data set is composed of amino acid composition, and the FASG, NISK, WOLS and KYTJ attribute data sets are composed of the amino acid composition and the auto-correlation functions of the corresponding amino acid residue index. The overall accuracies of SVM are 78.5, 87.5, 83.2, 81.7 and 81.9%, respectively, for COMP, FASG, NISK, WOLS and KYTJ data sets in jackknife test, which are 19.6, 7.8, 15.5, 13.1 and 15.8%, respectively, higher than that of the covariant discriminant algorithm in the same test. The results show that SVM may be applied to discriminate between the primary sequences of homodimers and non-homodimers and the two protein sequence descriptors can reflect the quaternary structure information. Compared with previous Robert Garian's investigation, the performance of SVM is almost equal to that of the Decision tree models, and the methods of extracting feature vector from the primary sequences are superior to Robert's binning function method.

Availability: Programs are available on request from the authors.
A random variance model for detection of differential gene expression in small microarray experiments
Authors: Wright George W. , Simon Richard M.
Published: December 2003

Motivation: Microarray techniques provide a valuable way of characterizing the molecular nature of disease. Unfortunately expense and limited specimen availability often lead to studies with small sample sizes. This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true.

Results: We propose a model by which the within gene variances are drawn from an inverse gamma distribution, whose parameters are estimated across all genes. This results in a test statistic that is a minor variation of those used in standard linear models. We demonstrate that the model assumptions are valid on experimental data, and that the model has more power than standard tests to pick up large changes in expression, while not increasing the rate of false positives.

Availability: This method is incorporated into BRB-ArrayTools version 3.0 (http://linus.nci.nih.gov/BRB-ArrayTools.html).

Supplementary material:  ftp://linus.nci.nih.gov/pub/techreport/RVM_supplement.pdf
KISS for STRAP: user extensions for a protein alignment editor
Authors: Gille Christoph , Lorenzen Stephan , Michalsky Elke , Frömmel Cornelius
Published: December 2003

Summary: The Structural Alignment Program STRAP is a comfortable comprehensive editor and analyzing tool for protein alignments. A wide range of functions related to protein sequences and protein structures are accessible with an intuitive graphical interface. Recent features include mapping of mutations and polymorphisms onto structures and production of high quality figures for publication. Here we address the general problem of multi-purpose program packages to keep up with the rapid development of bioinformatical methods and the demand for specific program functions. STRAP was remade implementing a novel design which aims at Keeping Interfaces in STRAP Simple (KISS). KISS renders STRAP extendable to bio-scientists as well as to bio-informaticians. Scientists with basic computer skills are capable of implementing statistical methods or embedding existing bioinformatical tools in STRAP themselves. For bio-informaticians STRAP may serve as an environment for rapid prototyping and testing of complex algorithms such as automatic alignment algorithms or phylogenetic methods. Further, STRAP can be applied as an interactive web applet to present data related to a particular protein family and as a teaching tool.

Requirements: JAVA-1.4 or higher.

Availability:  http://www.charite.de/bioinf/strap/
SNOW: Standard NOmenclature Wizard to help searching for (bio) chemical standardized names
Authors: Aguilar Daniel , Oliva Baldomero , Aviles Francesc X. , Querol Enrique
Published: December 2003

Summary: When developing bioinformatical tools dealing with enzymatic activity, metabolism or enzymatic networks, the problem of the lack of a clear nomenclature for biochemical compounds often arises. This problem leads us to develop a small web-based tool (SNOW, Standard NOmenclature Wizard) which may help to find recommended and trivial names or the correct closest spelling for a query compound name, if it exists.

Availability: Web-based interface available at http://ibb.uab.es/snow/

Supplementary information:  http://ibb.uab.es/snow/snow_moreinfo.html
Machaon CVE: cluster validation for gene expression data
Authors: Bolshakova Nadia , Azuaje Francisco
Published: December 2003

Summary: This paper presents a cluster validation tool for gene expression data. Machaon CVE (Clustering and Validation Environment) system aims to partition samples or genes into groups characterized by similar expression patterns, and to evaluate the quality of the clusters obtained.

Availability: The program is freely available for non-profit use on request at http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html

Supplementary information:  http://www.cs.tcd.ie/Nadia.Bolshakova/Machaon.html
DnaSP, DNA polymorphism analyses by the coalescent and other methods
Authors: Rozas Julio , Sánchez-DelBarrio Juan C. , Messeguer Xavier , Rozas Ricardo
Published: December 2003

Summary: DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (∼5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results.

Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp
A CART-based approach to discover emerging patterns in microarray data
Authors: Boulesteix Anne-Laure , Tutz Gerhard , Strimmer Korbinian
Published: December 2003

Motivation: Cancer diagnosis using gene expression profiles requires supervised learning and gene selection methods. Of the many suggested approaches, the method of emerging patterns (EPs) has the particular advantage of explicitly modeling interactions among genes, which improves classification accuracy. However, finding useful (i.e. short and statistically significant) EP is typically very hard.

Methods: Here we introduce a CART-based approach to discover EPs in microarray data. The method is based on growing decision trees from which the EPs are extracted. This approach combines pattern search with a statistical procedure based on Fisher's exact test to assess the significance of each EP. Subsequently, sample classification based on the inferred EPs is performed using maximum-likelihood linear discriminant analysis.

Results: Using simulated data as well as gene expression data from colon and leukemia cancer experiments we assessed the performance of our pattern search algorithm and classification procedure. In the simulations, our method recovers a large proportion of known EPs while for real data it is comparable in classification accuracy with three top-performing alternative classification algorithms. In addition, it assigns statistical significance to the inferred EPs and allows to rank the patterns while simultaneously avoiding overfit of the data. The new approach therefore provides a versatile and computationally fast tool for elucidating local gene interactions as well as for classification.

Availability: A computer program written in the statistical language R implementing the new approach is freely available from the web page http://www.stat.uni-muenchen.de/~socher/
Thrombin Preconditioning Attenuates Brain Edema Induced by Erythrocytes and Iron
Authors: Hua Ya , Keep Richard F. , Hoff Julian T. , Xi Guohua
Published: December 2003

Pretreatment with a low intracerebral dose of thrombin reduces brain edema after hemorrhagic and thromboembolic stroke. We have termed this phenomena thrombin preconditioning (TPC) or thrombin-induced brain tolerance. Red blood cell lysis and iron overload contribute to delayed edema formation after intracerebral hemorrhage. The present study examined whether TPC can attenuate the brain edema induced by lysed red blood cells or iron. It also examined whether TPC is associated with increasing hypoxia inducible factor-1α (HIF-1α) levels and alterations in two HIF-1α target genes, transferrin (Tf) and transferrin receptor (TfR), within the brain. Brain edema was measured by wet/dry weight method. HIF-1α, Tf, and TfR were measured by Western blot analysis and immunohistochemistry. We found that TPC reduces the edema induced by infusion of lysed red blood cells and iron. Thrombin increases HIF-1α levels through p44/42 mitogen activated protein kinases pathway. Thrombin also increases Tf and TfR levels in the brain. These results indicate that HIF-1α and its target genes may be involved in thrombin-induced brain tolerance.
Activation Systems for Latent Matrix Metalloproteinase-2 are Upregulated Immediately after Focal Cerebral Ischemia
Authors: Chang Dae-Il , Hosomi Naohisa , Lucero Jacinta , Heo Ji-Hoe , Abumiya Takeo , Mazar Andrew P. , del Zoppo Gregory J.
Published: December 2003

During focal cerebral ischemia, matrix metalloproteinase-2 (MMP-2) can contribute to the loss of microvessel integrity within ischemic regions by degrading the basal lamina. MMP-2 is secreted in latent form (pro-MMP-2), but the activation of pro-MMP-2 in the ischemic territory has not been shown. Immunohistochemical and in situ hybridization studies of the expression of the direct activators of MMP-2, MT1-MMP and MT3-MMP, and the indirect activation system tissue plasminogen activator, urokinase (u-PA), its receptor (u-PAR), and its inhibitor PAI-1 after middle cerebral artery occlusion/reperfusion were undertaken in basal ganglia samples from 26 adolescent male baboons. The expressions of all three MMPs, u-PA, u-PAR, and PA1-1, but not tissue plasminogen activator, were increased from 1 hour after middle cerebral artery occlusion in the ischemic core. mRNA transcripts confirmed the increases in latent MMP-2, u-PA, u-PAR, and PAI-1 antigen very early after middle cerebral artery occlusion. The expression patterns are consistent with secretion of pro-MMP-2 and its activators in the ischemic core, perhaps from separate cell compartments. The rapid and coordinate appearance of pro-MMP-2 and its activation apparatus suggest that in the primate striatum this protease may participate in matrix injury during focal cerebral ischemia.
Sequential Versus Nonsequential Measurement of Density and Affinity of Dopamine D2 Receptors with [11C]raclopride: Effect of Methamphetamine
Authors: Doudet Doris J. , Holden James E.
Published: December 2003

The multiple ligand concentration assays (MLCRA) method provides researchers with the ability to measure in vivo receptor characteristics in a stable condition. Measurements of the density and affinity of the dopamine D2 receptors with [11C]raclopride, using a sequential method (three scans throughout 1 day) or a nonsequential method (three scans spread over several weeks but at the same time of the day), yield similar values. However, after an acute challenge with drugs that affect dopamine neurotransmission, the concentration of endogenous ligand may vary over the course of the in vivo sequential MLCRA. Combined PET-microdialysis studies after acute amphetamine showed that during the imaging time frame the concentrations of extracellular dopamine vary widely, but that nonetheless the decrease in raclopride binding potential is sustained and nearly constant over time. These observations apparently contradict the simple competitive displacement model if the changes in extracellular concentration are taken to reflect necessarily comparable changes at the binding sites. To understand the effect of the delay between drug administration and start-to-end of data acquisition on the MLCRA results, we compared the outcomes of the sequential and nonsequential methods after methamphetamine. Comparison of the binding potential, density, and affinity of D2 receptors in both experimental conditions revealed good concordance between the data sets, suggesting that methamphetamine produces sustained and stable increases in synaptic dopamine.
Quantitative Cerebral Blood Flow Measurements in the Rat Using a Beta-Probe and H215O
Authors: Weber Bruno , Späth Nicolas , Wyss Matthias , Wild Damian , Burger Cyrill , Stanley Ross , Buck Alfred
Published: December 2003

Beta-probes are a relatively new tool for tracer kinetic studies in animals. They are highly suited to evaluate new positron emission tomography tracers or measure physiologic parameters at rest and after some kind of stimulation or intervention. In many of these experiments, the knowledge of CBF is highly important. Thus, the purpose of this study was to evaluate the method of CBF measurements using a beta-probe and H215O. CBF was measured in the barrel cortex of eight rats at baseline and after acetazolamide challenge. Trigeminal nerve stimulation was additionally performed in five animals. In each category, three injections of 250 to 300 MBq H215O were performed at 10-minute intervals. Data were analyzed using a standard one-tissue compartment model (K1 = CBF, k2 = CBF/p, where p is the partition coefficient). Values for K1 were 0.35 ± 0.09, 0.58 ± 0.16, and 0.49 ± 0.03 mL · min−1 · mL−1 at rest, after acetazolamide challenge, and during trigeminal nerve stimulation, respectively. The corresponding values for k2 were 0.55 ± 0.12, 0.94 ± 0.16, and 0.85 ± 0.12 min−7, and for p were 0.64 ± 0.05, 0.61 ± 0.07, and 0.59 ± 0.06. The standard deviation of the difference between two successive experiments, a measure for the reproducibility of the method, was 10.1%, 13.0%, and 5.7% for K1, k2, and p, respectively. In summary, beta-probes in conjunction with H215O allow the reproducible quantitative measurement of CBF, although some systematic underestimation seems to occur, probably because of partial volume effects.
Pixel-by-Pixel Spatiotemporal Progression of Focal Ischemia Derived Using Quantitative Perfusion and Diffusion Imaging
Authors: Shen Qiang , Meng Xiangjun , Fisher Marc , Sotak Christopher H. , Duong Timothy Q.
Published: December 2003

Pixel-by-pixel spatiotemporal progression of focal ischemia (permanent occlusion) in rats was investigated using quantitative perfusion and diffusion magnetic resonance imaging every 30 minutes for 3 hours. The normal left-hemisphere apparent diffusion coefficient (ADC) was 0.76 ± 0.03 × 10−3 mm2/s and CBF was 0.7 ± 0.3 mL · g−1 · min−1 (mean ± SD, n = 5). The ADC and CBF viability thresholds yielding the lesion volumes (LV) at 3 hours that best approximated the 2,3,5-triphenyltetrazolium chloride (TTC) infarct volumes (200 ± 30 mm2) at 24 hours were 0.53 ± 0.02 × 10−3 mm2/s (30% ± 2% reduction) and 0.30 ± 0.09 mL · g−1 · min−1 (57% ±11% reduction), respectively. Temporal evolution of the ADC- and CBF-defined LV showed a significant “perfusion-diffusion mismatch” up to 2 hours ( P < 0.05, n = 11), a potential therapeutic window. Based on the viability thresholds, three pixel clusters were identified on the CBF-ADC scatterplots: (1) a “normal” cluster with normal CBF and ADC, (2) an “ischemic core” cluster with markedly reduced CBF and ADC, and (3) a “mismatch” cluster with reduced CBF but slightly reduced ADC. These clusters were color-coded and mapped onto the image and CBF-ADC spaces. Lesions grew peripheral and medial to the initial ADC abnormality. In contrast to the CBF distribution, the ADC distribution in the ischemic hemisphere was bimodal; the relatively time-invariant bimodal-ADC minima were 0.57 ± 0.02 × 10−3 mm2/s (corresponding CBF 0.35 ± 0.04 mL · g−1 · min−1), surprisingly similar to the TTC-derived thresholds. Together, these results illustrate an analysis approach to systemically track the pixel-by-pixel spatiotemporal progression of acute ischemic brain injury.
Arg120stop nonsense mutation in the RP2 gene: mutational hotspot and germ line mosaicism?
Authors: Vorster AA , Rebello MT , Coutts N , Ehrenreich L , Gama AD , Roberts LJ , Goliath R , Ramesar R , Greenberg LJ
Published: December 2003

Mutations in the RP2 gene account for up to 20% of X‐linked recessive retinitis pigmentosa (RP). Arg120stop is to date the most frequently reported mutation found in RP2. Mutation screening was performed during the course of a large screening program of retinal degenerative disorders (RDDs) in South Africa using exon 1 and 2 of RP2 in 20 unrelated families with an X‐linked mode of retinal degenerative inheritance. Direct sequencing analysis revealed a C→T transition at position 358 in the proband in a family of German origin. Subsequent analysis revealed that this Arg120stop mutation cosegregated with the disease in an additional affected family member. The nonsense mutation, Arg120stop, could not however, be detected in the somatic cells of the obligate carrier female. This, the first report of a germ line mutation for a family with RP, has many implications for genetic counseling of retinal degeneration (RD). To avoid inaccurate risk assessment for RP due to epigenetic events, such as the rare occurrence of germ line mosaicism, genetic counseling in families with XLRP should always be guided by molecular testing.
Predictive testing for Huntington's disease: relationship with partners after testing
Authors: Decruyenaere M , Evers‐Kiebooms G , Cloostermans T , Boogaerts A , Demyttenaere K , Dom R , Fryns JP
Published: December 2003

This study focuses on the partner relationship of tested persons, 5 years after their predictive test result for Huntington's disease (HD). We describe changes in marital status, quality of the relationship, and perceived changes in the relationship. Twenty‐six carriers, 14 of their partners, 33 non‐carriers, and 17 of their partners participated in the study. Qualitative and quantitative methods were used. For the majority of tested persons (about 70%), the marital status was unchanged 5 years post test. Overall, carriers rated the quality of the relationship higher than their partners did and they perceived more positive changes. Qualitative data show that a test result leading to changed roles may induce significant marital distress. Another consequence of the test may be the changes in dynamics in asymptomatic carrier couples. A pre‐test discussion of the possible impact of the test result on the relationship should result in a better preparation for and more understanding of the reactions after testing. Counselling after testing should stimulate an open communication between partners with consideration of needs and anxieties of both partners.
Cytogenetic and molecular analysis of a family with three brothers afflicted with germ‐cell cancer
Authors: Ottesen AM , Rajpert‐De Meyts E , Holm M , Andersen I‐LF , Vogt PH , Lundsteen C , Skakkebæk NE
Published: December 2003

A thorough cytogenetic investigation and an analysis of detailed questionnaires were performed in a family with three brothers afflicted with germ‐cell tumors (GCTs), in an attempt to detect a congenital factor related either to a hereditary genetic background or an environmental/lifestyle influence. One brother had an intracranial tumor in the pineal region and the two others had testicular tumors. Peripheral blood was studied by traditional karyotyping, multicolor‐FISH, high‐resolution comparative genomic hybridization (HR‐CGH), and molecular analysis of selected loci on sex chromosomes (Yq11 region, TSPY, and the androgen receptor gene); however, no abnormalities were detected. The HR‐CGH analysis of microdissected histological components of the overt tumors and the adjacent carcinoma in situ demonstrated a pattern of genomic imbalances characteristic for sporadic GCTs, including gain of 12p. The questionnaire and interview revealed a history of different cancers in the extended family, and a possible in utero and/or infantile exposure of the three brothers with GCTs to compounds suspected of endocrine‐disrupting properties. Although no genetic aberration was detected in this family, we suspect the presence of a recessive hereditary factor pre‐disposing to cancer, which probably was manifested as GCTs in the three brothers because of an adverse effect of an environmental factor on the early germ‐cell differentiation.
Willingness to donate blood samples for genetic research: a survey from a community in Singapore
Authors: Wong ML , Chia KS , Yam WM , Teodoro GR , Lau KW
Published: December 2003

Studies on the public's willingness to donate blood specimens for genetic research are few and are conducted mainly among Western countries. Little is known about the Asian community's willingness to participate in genetic research. A community‐based survey was conducted on 548 adult Singaporeans to examine their willingness to donate blood samples for genetic research and its associated factors. The response rate was 70.3%. About 49.3% (95% CI, 45.1–53.5%) were willing to donate blood for genetic research. In the multivariable Cox regression analysis, willingness was significantly associated with belief in the benefits of genetic research; intention to participate in government studies; having no fear of pain, blood, injections, and needles; and non‐concern about the loss of confidentiality. Reasons against donating blood were fear of pain, blood, injections, and needles (38.1%); no self‐benefits (24.8%); fear of finding out about having a disease (22.3%); fear of discrimination (18.7%); and concerns about weakness (15.1%) and weight gain (9.4%). Public education programs to promote participation in genetic research should stress its benefits and address people's fears and concerns.
Contested rainforests, NGOs, and projects of desire in Solomon Islands
Authors: Hviding Edvard
Published: December 2003

This paper examines what the author terms “compressed globalisation” in the South Pacific region, with a focus on the Solomon Islands. Building on long‐term ethnographic fieldwork in the biodiversity “hot‐spot” of Marovo Lagoon, the author addresses the complexity of a variety of local–global encounters during the 1990s, involving indigenous resource‐owning villagers, transnational logging and mining companies, and foreign conservationist initiatives by non‐governmental organisations (NGOs). Emphasis is given to the contested status of rainforests around the Marovo Lagoon. While Asian logging companies desire quick exploitation of large timber reserves, Western NGOs (and similar governmental agencies) desire the conservation of the forests in the name of global biodiversity. The villagers who own the forests through state‐backed customary law follow unpredictable paths between the diverging types of foreign (and global) desire, emphasising their own autonomy over conditions for contemporary village life. These postcolonial encounters are characterised by mutual uncertainty and unawareness about the moral and political agendas of the “other party”. However, lack of shared understanding far from inhibits actual collaboration, whether it be short‐term logging deals or NGO‐initiated “community‐based conservation projects”. In these projects, defined through indigenous concepts, diverging desires appear to converge, however unsteadily.