bluuebunny/crossref_metadata_2025 huggingface dataset:
Genesis of the Kapuskasing (Ontario) migmatitic mafic granulites by dehydration melting of amphibolite: the importance of quartz to reaction progress
Authors: HARTEL T. H. D. , PATTISON D. R. M.
Published: November 2003

Migmatitic, granulite‐grade mafic gneisses make up a significant part of the Kapuskasing Structural Zone (KSZ), Ontario. Although they contain a common mineral assemblage [hornblende (Hbl)+plagioclase (Pl)+diopside (Di)±garnet (Grt)+quartz (Qtz)±titanite (Ttn)], the mafic gneisses show wide variations in modal mineralogy from hornblende‐rich to diopside+garnet‐rich varieties and all gradations between. Up to 25 vol.% segregated plagioclase+quartz‐rich (trondhjemitic) leucosome (Tdh) is intimately associated with the mafic gneiss, occurring in a continuum of patches, veins and transecting dykes at scales ranging from decimetres to micrometres. The texture and composition of the leucosome, combined with P‐T  estimates for the host rocks above the solidus, suggest it represents crystallized trondhjemitic melt. Quartz is mainly restricted to the segregated leucosomes but more rarely occurs in a variety of interstitial textures in the mafic gneiss, suggesting that it crystallized from a melt phase rather than having been present as a solid phase at peak metamorphic conditions. Modal and textural data indicate a reaction relationship of the form: Hbl+Pl(+Qtz?)=Grt+Di+Ttn+leucosome (Tdh), implying that the granulite‐forming process involved dehydration melting of an amphibolite protolith. Pressure‐temperature estimates from Grt+Di+Pl+Qtz geothermobarometry are 9 kbar and 685‐735 °C; however, based on experimental studies of dehydration melting of amphibolite, we estimate that peak conditions were closer to 11 kbar, 850 °C. Mass balance analysis, using the technique of singular value decomposition, and reaction space analysis were used to quantify the reaction and to determine the controls on reaction progress. The following mass balance provides a model for the natural reaction:1.00 Hbl+0.92 Pl+3.76 Qtz=1.14 Grt+1.54 Di+0.21 Ttn+1.49 Tdh+0.14 ‘pg’+0.39 Fe−1Mg+0.33 NaSiCa−1Al−1where ‘pg’ is a pargasite‐like exchange. In all model mass balances tested, quartz is a reactant with a large coefficient. We argue that the abundance of quartz in the amphibolite protolith was the primary control on the differing extents of reaction observed. Mineral compositional variation exerted a secondary control on reaction progress, with Fe‐richer layers containing An‐richer plagioclase and more actinolitic amphibole reacting earliest (i.e. at lowest temperatures). Comparison of the calculated amount of melt produced in the gneisses with that now observed implies expulsion of 5–30% of the melt. These volumes are similar to those predicted from REE modelling of Archaean tonalities and trondhjemites from a garnet amphibolite source, suggesting that the KSZ mafic gneisses may be representative of partially depleted source rocks for trondhjemite‐tonalite generation.
Prism‐ and basal‐plane parallel subgrain boundaries in quartz: a microstructural geothermobarometer
Authors: KRUHL J. H.
Published: November 2003

Empirical data on quartz subgrain patterns from various metamorphic rocks show that, at least up to 10 kbar in the stability field of low‐quartz, prismatic subgrain boundaries are dominant whereas basal subgrain boundaries are not developed. In the high‐quartz stability field, both prismatic and basal subgrain boundaries occur and form typical rectangular (‘chessboard’) patterns. The likely reason behind the different occurrence of these subgrain patterns is that in high‐quartz prismatic glide becomes as easy as, or probably even easier than, basal glide. The two types of subgrain patterns can be clearly distinguished by optical microscopy. Consequently, the occurrence of chessboard subgrain patterns in quartz represents a practicable geothermobarometer. The possibilities of its application are far reaching and include the specification of deformation conditions at high‐grade metamorphism, the recognition of syntectonic intrusions and the distinction between pluton emplacement at lower and at higher crustal levels.
Pervasive granitoid magma transfer through the lower–middle crust during non‐coaxial compressional deformation
Authors: COLLINS W. J. , SAWYER E. W.
Published: November 2003

Granitic magmas migrated through Early Proterozoic middle–lower crust at Mt Hay, central Australia, via a diverse network of narrow structurally controlled channelways, during a period of progressive W–SW‐directed thrusting (D1a–D1d). They utilized existing folds, boudins and shear zones, or created new channels by magmatic fracture either parallel to layering or, rarely, in irregular arrays. The magmas rose obliquely, parallel to the plunging (50–60°) regional elongation direction, which was defined by coaxial folds, boudin necks and a strong mineral‐elongation lineation. Megacrystic charnockitic magmas migrated through metre‐scale conduits during D1a–D1b, but leucosomes were generally restricted to smaller (centimetre‐scale) structures that existed throughout the entire deformation history. Thus, D1a/D1b leucosomes were potential feeders of in situ partial melts to the adjacent larger conduits of charnockite magma, thereby providing a pervasive interconnected network that allowed efficient migration of all magma types during the early stages of thrusting.

The upper–middle crust of the Anmatjira–Reynolds Range area contains abundant megacrystic granitoid sheets that are of similar age and geochemistry to those at Mt Hay. They are considered to have formed as syntectonic intrusions emplaced during W–SW‐directed thrusting, as at Mt Hay, suggesting that granitic magmas formed near the base of the continental crust passed through the mid‐lower crustal level (25–30 km) exposed at Mt Hay and accumulated, in batholithic proportions, at shallower crustal levels (12–20 km) such as the Anmatjira–Reynolds Range area.

The observations imply that granitoid magmas in the deep crust are capable of pervasive migration through the crust during major compressive, noncoaxial shear deformation. Localization of magmas by sequentially developed, narrow, compressive structures suggests that dilatancy followed successive foliation‐forming events, a situation that can occur during steady‐state deformation if the effective confining pressures are low, which would be a result of high and possibly variable rates of magma influx. The inferred rapid melt segregation and migration during deformation suggest that large chambers do not form until magma reaches neutral buoyancy in the middle to upper continental crust.
High‐pressure granulites from the Sudetes (south‐west Poland): evidence of crustal subduction and collisional thickening in the Variscan Belt
Authors: KRYZA R. , PIN C. , VIELZEUF D.
Published: November 2003

Two high‐grade gneissic complexes of the Western Sudetes, the Góry Sowie Block and the Śnieżnik area complex, contain small, predominantly felsic granulitic inliers with minor Cpx‐bearing intercalations. The P–T  conditions of the granulite facies events and of the subsequent re‐equilibration are estimated using the ternary feldspar thermometer and the Geo‐Calc computer program (version TWQ, Jan 92).

In the Góry Sowie granulites, the peak granulitic event occurred at c. 18–20 kbar and 900 °C, and the late decompressive re‐equilibration within a range of 4–10 kbar and temperatures decreasing to 600–700 °C. The latter event is thought to have coincided with the main metamorphic phase in the surrounding gneisses.

The P–T  estimates are more scattered in the Śnieżnik granulites, but the peak conditions for the granulitic event are estimated at pressure over 22 kbar (possibly around 30 kbar) and temperature exceeding 900 °C. The analysed samples from the Śnieżnik area bear no significant evidence of lower‐pressure re‐equilibration.

Integrating the thermobarometric data and some age constraints indicates that the Góry Sowie granulites belong to the early stage ‘type I’ granulites of the Variscan Belt (c. 400 Ma old), which are interpreted as fragments of continental crustal materials subducted to mantle depths in the earliest stages of the Variscan orogeny. The Śnieżnik granulites are more problematic; they may belong to a ‘younger high‐P suite’ (c. 350 Ma old), widespread in the southern and eastern parts of the Bohemian Massif, and possibly related to the climax of the Variscan continent–continent collision.
Problems with inferring P–T–t paths in low‐P granulite facies rocks
Authors: VERNON R. H.
Published: November 2003

Microstructural evidence commonly is used to infer metamorphic reactions, which are used to infer pressure–temperature–time (P–T–t) paths. However, this approach in low‐P/high‐T  (LPHT) granulite facies metamorphic terranes has two main problems. (1) Microstructural evidence may be inconclusive, so that reactions cannot be inferred with confidence. In particular, relative timing of mineral growth inferred from inclusions, moulding relationships and foliation–porphyroblast relationships is commonly ambiguous or invalid. The most reliable indicators of metamorphic reactions are partial pseudomorphs and corona structures, especially if symplectic intergrowths (indicating simultaneous growth of two or more minerals) are involved. (2) Even reactions that can be inferred with confidence do not indicate unique P–T  trends, owing to P–T  slopes of reaction curves. Where successive reactions can be shown to have occurred in the same rock, a line or curve joining reaction‐curve intersections gives an apparent single‐event path. However, isotopic evidence is needed to prove that polymetamorphism (involving more complex paths making fortuitous intersections with the apparent single‐event path) did not occur. Although these problems are well known, their importance is not always emphasized in metamorphic investigations.

The difficulties are illustrated by published work on P–T–t paths for Proterozoic LPHT granulite facies rocks of central Australia and Antarctica. Recent work in Antarctica has shown that P–T–t paths may be episodic and more complex than the simple, single‐event paths commonly inferred from microstructural evidence alone.
Rare earth and other trace element mobility during mylonitization: a comparison of the Brevard and Hope Valley shear zones in the Appalachian Mountains, USA
Authors: CONDIE K. C. , SINHA A. K.
Published: November 2003

In progressing from a granitoid mylonite to an ultramylonite in the Brevard shear zone in North Carolina, Ca and LOI (H2O) increase, Si, Mg, K, Na, Ba, Sr, Ta, Cs and Th decrease, while changes in Al, Ti, Fe, P, Sc, Rb, REE, Hf, Cr and U are relatively small. A volume loss of 44% is calculated for the Brevard ultramylonite relative to an Al–Ti–Fe isocon. The increase in Ca and LOI is related to a large increase in retrograde epidote and muscovite in the ultramylonite, the decreases in K, Na, Si, Ba and Sr reflect the destruction of feldspars, and the decrease in Mg is related to the destruction of biotite during mylonitization. In an amphibolite facies fault zone separating grey and pink granitic gneisses in the Hope Valley shear zone in New England, compositional similarity suggests the ultramylonite is composed chiefly of the pink gneisses. Utilizing an Al–Ti–Fe isocon for the pink gneisses, Sc, Cr, Hf, Ta, U, Th and M‐HREE are relatively unchanged, Si, LOI, K, Mg, Rb, Cs and Ba are enriched, and Ca, Na, P, Sr and LREE are lost during deformation. In contrast to the Brevard mylonite, the Hope Valley mylonite appears to have increased in volume by about 70%, chiefly in response to an introduction of quartz.

Chondrite‐normalized REE patterns of granitoids from both shear zones are LREE‐enriched and have prominent negative Eu anomalies. Although REE increase in abundance in the Brevard ultramylonites (reflecting the volume loss), the shape of the REE pattern remains unchanged. In contrast, REE and especially LREE decrease in abundance with increasing deformation of the Hope Valley gneisses. Mass balance calculations indicate that ≥95% of the REE in the Brevard rocks reside in titanite. In contrast, in the Hope Valley rocks only 15–40% of the REE can be accounted for collectively by titanite, apatite and zircon. Possible sites for the remaining REE are allanite, fluorite or grain boundaries. Loss of LREE from the pink gneisses during deformation may have resulted from decreases in allanite and perhaps apatite or by leaching ofy REE from grain boundaries by fluids moving through the shear zone.

Among the element ratios most resistant to change during mylonitization in the Brevard shear zone are La/Yb, Eu/Eu*, Sm/Nd, La/Sc, Th/Sc, Th/Yb, Cr/Th, Th/U and Hf/Ta, whereas the most stable ratios in the Hope Valley shear zone are K/Rb, Rb/Cs, Th/U, Eu/Eu*, Th/Sc, Th/Yb, Sm/Nd, Th/Ta, Hf/Ta and Hf/Yb. However, until more trace element data are available from other shear zones, these ratios should not be used alone to identify protoliths of deformed rocks.
Temperature–time path for the low‐pressure Ryoke metamorphism, Japan, based on chemical zoning in garnet
Authors: OKUDAIRA T.
Published: November 2003

Garnet crystals from low‐pressure/high‐temperature (LPHT) Ryoke metamorphic rocks in the Yanai district, south‐western Japan, show several kinds of chemical zoning patterns that systematically vary with grain radius between c. 0.1 and 0.5 mm. Large grains (>c. 0.4 mm) show normal zoning and small grains (<c. 0.4 mm) show unzoned or reversely zoned cores. Observations of the chemical zoning and of the spatial and size distributions of the garnet grains between c. 0.1 and 0.5 mm in radius suggest that they were formed by continuous nucleation and diffusion‐controlled growth.

A previously estimated temperature–time path (T –t path) for the Ryoke metamorphism, using 1‐D numerical simulation, is characterized by a rapid increase in temperature, 0.0017 °C yr−1 on average, and a period of high temperature (>600 °C) shorter than 0.5 Myr, which was presumably caused by the intrusion of a granodiorite sheet. Chemical zoning of garnet grains with different radii simulated for the T –t path using a numerical model of continuous nucleation and diffusion‐controlled growth, in combination with intracrystalline diffusion, compares well with the observed zoning patterns in garnet grains with different radii. This is in spite of the fact that the simulated zoning patterns vary greatly, depending on subtle differences in the T–t history. Therefore, they suggest that the T–tpath gives a good explanation for the LPHT Ryoke metamorphism. Although this study only refers to the Ryoke metamorphism, the technique may be applicable to thermal modelling of other metamorphic terranes.
Garnet Sm–Nd data from the Saualpe and the Koralpe (Eastern Alps, Austria): chronological and P–T constraints on the thermal and tectonic history
Authors: THÖNI M. , MILLER CH.
Published: November 2003

Garnets from recrystallized, staurolite‐ and kyanite‐bearing mica schists from the central Saualpe basement, representing the host rocks of the type‐locality eclogites, give concordant Sm–Nd garnet–whole‐rock isochron ages between 88.5±1.7 and 90.9±0.7 Ma. The millimetre‐sized, mostly inclusion‐free grains show fairly homogeneous element profiles with pyrope contents of 25–27%. Narrow rims with an increase in Fe and Mn and a decrease in Mg document minor local re‐equilibration during cooling. According to phengite geothermobarometry, peak metamorphic conditions at 90 Ma were close to 20 kbar and 680 °C and similar to those recorded by the eclogites. The garnet rims record about 575 °C/7 kbar for the final stages of metamorphism. A phengitic garnet–mica schist, sampled at the immediate contact with the Gertrusk eclogite, gave a garnet–whole‐rock Sm–Nd age of 94.0±2.7 Ma.

Garnet porphyroclasts separated from a pegmatite–mylonite of the Koralpe plattengneiss near Stainz are unzoned and show spessartine contents of 15%. Composition and Sm–Nd ages of close to 260 Ma point to a magmatic origin for these garnets.

The garnet data from the Saualpe document an intense Alpine metamorphism for this part of the Austroalpine basement. The mica schists recrystallized during decompression and rapid exhumation, at the final stages of and immediately following a high‐P event. The Koralpe data show that high Alpine temperatures did not reopen the Sm–Nd isotope system, implying a closure temperature in excess of c. 600 °C for this isotopic system in garnet.
Hydration of orthopyroxene–cordierite‐bearing assemblages at Laouni, Central Hoggar, Algeria
Authors: GUIRAUD M. , POWELL R. , COTTIN J.‐Y.
Published: November 2003

In the Laouni region (Central Hoggar, Algeria), retrogression of high‐grade orthopyroxene–cordierite‐bearing rocks led to the crystallization of orthoamphibole and garnet, and at a later stage of chlorite, from the original paragenesis. Calculated phase diagrams show that this retrogression occurred at about 3 kbar with the simplest model involving hydration at 650–700° C and at around 500° C, with the rocks experiencing aH2O less than 1, except possibly in the last stages of chlorite crystallization. As the other rock types occurring in the same area as the orthopyroxene–cordierite rocks display similar features, it is concluded that regional hydration occurred, presumably related to the release of fluids during the crystallization of the Pan‐African granitic and mafic magmas that are widespread in the Laouni area.
Magmatic arc metamorphism: petrology and temperature history of metabasic rocks in the Coastal Cordillera of northern Chile
Authors: LUCASSEN F. , FRANZ G.
Published: November 2003

We investigated the metamorphic cooling history of underplated magmatic rocks at midcrustal depth. Granulites and amphibolites occur within the Jurassic magmatic belt of the Coast Range south of Antofagasta in northern Chile between 23°25′ and 24°20′ S. The protoliths of the metamorphic rocks are basic intrusions of Early Mesozoic age. They are part of the magmatically formed crust, and the essentially dry magmas were emplaced in an extensional regime. The granulites (clinopyroxene–orthopyroxene–plagioclase) show all stages of fabric development from magmatic to granoblastic fabrics. Pyroxene compositions were reset at temperatures around 800° C independent of the stage of textural equilibration. The granulites were partially amphibolitized at upper amphibolite facies temperatures of 600–700° C. Following cooling, a possible reheating to greenschist facies temperatures around 500° C is indicated by prograde zoning in magnetite–ilmenite pairs. Mineral assemblages are not suitable for barometry, but a conservative estimation of the garnet‐in reaction at given whole‐rock compositions suggests maximum pressures in the granulite facies of around 5 kbar, and similar pressures are indicated by phengite barometry for the greenschist facies. The P–T  path of granulite–amphibolite metamorphism is one of slow cooling from magmatic temperatures with heterogeneous deformation. The thinning of the pre‐Andean (Precambrian–Triassic) crust was apparently compensated by the magmatic underplating and this special tectonomagmatic setting caused the prolonged residence of the accreted rocks at midcrustal levels.
Pattern Recognition with the Optic Nerve Visual Prosthesis
Authors: Veraart Claude , Wanet‐Defalque Marie‐Chantal , Gérard Benoît , Vanlierde Annick , Delbeke Jean
Published: November 2003

Abstract:  A volunteer with retinitis pigmentosa and no residual vision was chronically implanted with an optic nerve electrode connected to an implanted neurostimulator and antenna. An external controller with telemetry was used for electrical activation of the nerve which resulted in phosphene perception. Open‐loop stimulation allowed the collection of phosphene attributes and the ability to elicit perception of simple geometrical patterns. Low perception thresholds allowed for large current intensity range within safety limits. In a closed‐loop paradigm, the volunteer was using a head‐worn video camera to explore a projection screen. The volunteer underwent performance evaluation during the course of a training program with 45 simple patterns. After learning, the volunteer reached a recognition score of 63% with a processing time of 60 s. Mean performance in orientation discrimination reached 100% with a processing time of 8 s.
MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis
Authors: Lee Dong-Yup , Yun Hongsoek , Park Sunwon , Lee Sang Yup
Published: November 2003

Summary: MetaFluxNet is a program package for managing information on the metabolic reaction network and for quantitatively analyzing metabolic fluxes in an interactive and customized way. It allows users to interpret and examine metabolic behavior in response to genetic and/or environmental modifications. As a result, quantitative in silico simulations of metabolic pathways can be carried out to understand the metabolic status and to design the metabolic engineering strategies. The main features of the program include a well-developed model construction environment, user-friendly interface for metabolic flux analysis (MFA), comparative MFA of strains having different genotypes under various environmental conditions, and automated pathway layout creation.

Availability:  http://mbel.kaist.ac.kr/

Supplementary information: A manual for MetaFluxNet is available as PDF file.
LDA—a java-based linkage disequilibrium analyzer
Authors: Ding Keyue , Zhou Kaixin , He Fuchu , Shen Yan
Published: November 2003

Summary: We describe an integrated java-based program that provides elaborate graphic and plain-text output of pairwise linkage disequilibrium (LD) analysis of single nucleotide polymorphisms genotypic data. It is most suitable for molecular geneticists, who are focusing on LD measures estimation, statistical significance test and extent prediction.

Availability: The software is available at: http://www.chgb.org.cn/lda/lda.htm

Supplementary information: Detailed tutorials, LDA help system and examples are distributed within LDA software. For Macintosh OS X user, the Jre version 1.4 can be downloaded from http://connect.apple.com
Inferring protein interactions from phylogenetic distance matrices
Authors: Gertz Jason , Elfond Georgiy , Shustrova Anna , Weisinger Matt , Pellegrini Matteo , Cokus Shawn , Rothschild Bruce
Published: November 2003

Finding the interacting pairs of proteins between two different protein families whose members are known to interact is an important problem in molecular biology. We developed and tested an algorithm that finds optimal matches between two families of proteins by comparing their distance matrices. A distance matrix provides a measure of the sequence similarity of proteins within a family. Since the protein sets of interest may have dozens of proteins each, the use of an efficient approximate solution is necessary. Therefore the approach we have developed consists of a Metropolis Monte Carlo optimization algorithm which explores the search space of possible matches between two distance matrices. We demonstrate that by using this algorithm we are able to accurately match chemokines and chemokine-receptors as well as the tgfβ family of ligands and their receptors.
Venn Mapping: clustering of heterologous microarray data based on the number of co-occurring differentially expressed genes
Authors: Smid Marcel , Dorssers Lambert C.J. , Jenster Guido
Published: November 2003

Motivation: To evaluate microarray data, clustering is widely used to group biological samples or genes. However, problems arise when comparing heterologous databases. As the clustering algorithm searches for similarities between experiments, it will most likely first separate the data sets, masking relationships that exist between samples from different databases.

Results: We developed a program, Venn Mapper, to calculate the statistical significance of the number of co-occurring differentially expressed genes in any of the two experiments. For proof of principle, we analysed a heterologous data set of 170 microarrays including breast and prostate cancer microarray analyses. Significant overlap was found in an unsupervised analysis between metastasized prostate cancer and metastasized breast cancer and BRCA mutated breast cancer. A comparison between single microarray data and the averaged breast and prostate data sets was also evaluated. This analysis suggests that genes expressed higher in stromal cells are also implicated in metastatic prostate cancer and BRCA mutated breast cancer. The Venn Mapper program identifies overlaps between samples from heterologous data sets and directly extracts the genes responsible for the overlap. From this information novel biological hypotheses may be addressed.

Availability: Venn Mapper is freely available on http://www.erasmusmc.nl/gatcplatform

Supplementary information:  http://www.erasmusmc.nl/gatcplatform/vennmapper.html
Linear regression and two-class classification with gene expression data
Authors: Huang Xiaohong , Pan Wei
Published: November 2003

Motivation: Using gene expression data to classify (or predict) tumor types has received much research attention recently. Due to some special features of gene expression data, several new methods have been proposed, including the weighted voting scheme of Golub et al., the compound covariate method of Hedenfalk et al. (originally proposed by Tukey), and the shrunken centroids method of Tibshirani et al. These methods look different and are more or less ad hoc.

Results: We point out a close connection of the three methods with a linear regression model. Casting the classification problem in the general framework of linear regression naturally leads to new alternatives, such as partial least squares (PLS) methods and penalized PLS (PPLS) methods. Using two real data sets, we show the competitive performance of our new methods when compared with the other three methods.
A Bayesian missing value estimation method for gene expression profile data
Authors: Oba Shigeyuki , Sato Masa-aki , Takemasa Ichiro , Monden Morito , Matsubara Ken-ichi , Ishii Shin
Published: November 2003

Motivation: Gene expression profile analyses have been used in numerous studies covering a broad range of areas in biology. When unreliable measurements are excluded, missing values are introduced in gene expression profiles. Although existing multivariate analysis methods have difficulty with the treatment of missing values, this problem has received little attention. There are many options for dealing with missing values, each of which reaches drastically different results. Ignoring missing values is the simplest method and is frequently applied. This approach, however, has its flaws. In this article, we propose an estimation method for missing values, which is based on Bayesian principal component analysis (BPCA). Although the methodology that a probabilistic model and latent variables are estimated simultaneously within the framework of Bayes inference is not new in principle, actual BPCA implementation that makes it possible to estimate arbitrary missing variables is new in terms of statistical methodology.

Results: When applied to DNA microarray data from various experimental conditions, the BPCA method exhibited markedly better estimation ability than other recently proposed methods, such as singular value decomposition and K-nearest neighbors. While the estimation performance of existing methods depends on model parameters whose determination is difficult, our BPCA method is free from this difficulty. Accordingly, the BPCA method provides accurate and convenient estimation for missing values.

Availability: The software is available at http://hawaii.aist-nara.ac.jp/~shige-o/tools/
Kernel hierarchical gene clustering from microarray expression data
Authors: Qin Jie , Lewis Darrin P. , Noble William Stafford
Published: November 2003

Motivation: Unsupervised analysis of microarray gene expression data attempts to find biologically significant patterns within a given collection of expression measurements. For example, hierarchical clustering can be applied to expression profiles of genes across multiple experiments, identifying groups of genes that share similiar expression profiles. Previous work using the support vector machine supervised learning algorithm with microarray data suggests that higher-order features, such as pairwise and tertiary correlations across multiple experiments, may provide significant benefit in learning to recognize classes of co-expressed genes.

Results: We describe a generalization of the hierarchical clustering algorithm that efficiently incorporates these higher-order features by using a kernel function to map the data into a high-dimensional feature space. We then evaluate the utility of the kernel hierarchical clustering algorithm using both internal and external validation. The experiments demonstrate that the kernel representation itself is insufficient to provide improved clustering performance. We conclude that mapping gene expression data into a high-dimensional feature space is only a good idea when combined with a learning algorithm, such as the support vector machine that does not suffer from the curse of dimensionality.

Availability: Supplementary data at www.cs.columbia.edu/compbio/hiclust. Software source code available by request.
Pathway studio—the analysis and navigation of molecular networks
Authors: Nikitin Alexander , Egorov Sergei , Daraselia Nikolai , Mazo Ilya
Published: November 2003

Summary: PathwayAssist is a software application developed for navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules.

Availability: PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/
GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic data
Authors: Martínez-Cruz Luis A. , Rubio Angel , Martínez-Chantar María L. , Labarga Alberto , Barrio Isabel , Podhorski Adam , Segura Victor , Sevilla Campo José L. , Avila Matías A. , Mato Jose M.
Published: November 2003

Summary: Genomic Analysis and Rapid Biological ANnotation (GARBAN) is a new tool that provides an integrated framework to analyze simultaneously and compare multiple data sets derived from microarray or proteomic experiments. It carries out automated classifications of genes or proteins according to the criteria of the Gene Ontology Consortium at a level of depth defined by the user. Additionally, it performs clustering analysis of all sets based on functional categories or on differential expression levels. GARBAN also provides graphical representations of the biological pathways in which all the genes/proteins participate.

Availability:  http://garban.tecnun.es
Beyond the Debate: Why Some Adolescents Report Stable Self‐Worth Over Time and Situation, Whereas Others Report Changes in Self‐Worth
Authors: Harter Susan , Whitesell Nancy R.
Published: November 2003

Abstract Within the field of personality and social psychology, there has been historical controversy over whether constructs such as self‐esteem are stable over time and situation or whether they are changeable. One response to this question has been to invoke two types of self‐esteem or self‐worth, trait self‐esteem and state self‐esteem. Thus it has been asserted that adolescents, the participants in this paper, have both a baseline self‐esteem as well as a barometric self‐esteem that represents short‐term fluctuations (Rosenberg, 1986). In this paper, we contend that constructs such as self‐esteem are not, in and of themselves, trait‐like or state‐like in nature. Rather, certain individuals display trait‐like behavior, whereas others demonstrate change in self‐esteem or self‐worth across relatively long periods of time, on a short‐term basis, and across situations. Three studies document these claims. The first addresses self‐worth as a function of the transition from high school to college. The second examines short‐term fluctuations in self‐worth. The third investigates variability in self‐worth across relational contexts, namely, relational self‐worth. In each study, findings reveal that certain adolescents report stability in self‐worth whereas others report change, fluctuations, or variability. Social causes of these individual differences are identified in each study, as are mental health implications. It is argued that such approaches provide a clearer understanding of the complexity of self‐processes.
The Relations of Effortful Control and Reactive Control to Children's Externalizing Problems: A Longitudinal Assessment
Authors: Valiente Carlos , Eisenberg Nancy , Smith Cynthia L. , Reiser Mark , Fabes Richard A. , Losoya Sandra , Guthrie Ivanna K. , Murphy Bridget C.
Published: November 2003

Abstract
In this study, we examined the role of negative emotionality as a moderator of the relations of effortful control and overcontrol (versus undercontrol) with children's externalizing problem behaviors; we also examined the longitudinal relations among these variables. Teachers' and parents' reports of children's negative emotionality, effortful control, overcontrol and externalizing problem behaviors were obtained at T1 (N=199; M age=89.51 months) and again 2 (T2) and 4 years (T3) later. In addition, children's effortful control was assessed with an observed measure of persistence. In a T3 concurrent structural equation model, effortful control, but not overcontrol, was negatively related to children's T3 externalizing problem behaviors. In regression analyses, the negative relation between T3 effortful control and externalizing problem behaviors was strongest at high levels of T3 negative emotionality. In the best‐fitting longitudinal structural equation model, both T1 effortful control and T1 overcontrol negatively predicted externalizing problems at T1, whereas T3 effortful control (but not T3 overcontrol) was significantly negatively related to T3 externalizing problem behaviors when controlling for T1 externalizing problem behaviors.
The History of Sexual Anatomy and Self‐Referential Philosophy of Science
Authors: Soble Alan G.
Published: November 2003

This essay is a case study of the self‐destruction that occurs in the work of a social‐constructionist historian of science who embraces a radical philosophy of science. It focuses on Thomas Laqueur's Making Sex: Body and Gender from the Greeks to Freud in arguing that a history of science committed to the social construction of science and to the central theses of Kuhnian, Duhemian, and Quinean philosophy of science is incoherent through self‐reference. Laqueur's text is examined in detail in order to make the main point; a similar phenomenon in the work of the feminist historian of science Evelyn Fox Keller is then briefly discussed.
Analytic and Continental Philosophy: Explaining the Differences
Authors: Levy Neil
Published: November 2003

A number of writers have tackled the task of characterizing the differences between analytic and Continental philosophy. I suggest that these attempts have indeed captured the most important divergences between the two styles but have left the explanation of the differences mysterious. I argue that analytic philosophy is usefully seen as philosophy conducted within a paradigm, in Kuhn's sense of the word, whereas Continental philosophy assumes much less in the way of shared presuppositions, problems, methods and approaches. This important opposition accounts for all those features that have rightly been held to constitute the difference between the two traditions. I finish with some reflections on the relative superiority of each tradition and by highlighting the characteristic deficiencies of each.
Shades of Orientalism: Paradoxes and Problems in Indian Historiography
Authors: Heehs Peter
Published: November 2003

In Orientalism, Edward Said attempts to show that all European discourse about the Orient is the same, and all European scholars of the Orient complicit in the aims of European imperialism. There may be “manifest” differences in discourse, but the underlying “latent” orientalism is “more or less constant.” This does not do justice to the marked differences in approach, attitude, presentation, and conclusions found in the works of various orientalists. I distinguish six different styles of colonial and postcolonial discourse about India (heuristic categories, not essential types), and note the existence of numerous precolonial discourses. I then examine the multiple ways exponents of these styles interact with one another by focusing on the early‐twentieth‐century nationalist orientalist, Sri Aurobindo. Aurobindo's thought took form in a colonial framework and has been used in various ways by postcolonial writers. An anti‐British nationalist, he was by no means complicit in British imperialism. Neither can it be said, as some Saidians do, that the nationalist style of orientalism was just an imitative indigenous reversal of European discourse, using terms like “Hinduism” that had been invented by Europeans. Five problems that Aurobindo dealt with are still of interest to historians: the significance of the Vedas, the date of the vedic texts, the Aryan invasion theory, the Aryan‐Dravidian distinction, and the idea that spirituality is the essence of India. His views on these topics have been criticized by Leftist and Saidian orientalists, and appropriated by reactionary “Hindutva” writers. Such critics concentrate on that portion of Aurobindo's work which stands in opposition to or supports their own views. A more balanced approach to the nationalist orientalism of Aurobindo and others would take account of their religious and political assumptions, but view their project as an attempt to create an alternative language of discourse. Although in need of criticism in the light of modern scholarship, their work offers a way to recognize cultural particularity while keeping the channels of intercultural dialogue open.
An Appeal from the New to the Old Historicists
Authors: Ankersmit F. R.
Published: November 2003

Book reviewed in this article:

Jürgen Pieters, Moments Of Negotiation: The New Historicism Of Stephen Greenblatt
Investor Response to Cash Flow Information
Authors: Garrod Hadi Neil, Mahdi
Published: November 2003

In this study the usefulness of cash flow data as required by the UK standard, FRS1, is evaluated and cash flow per share is investigated as a possible specification of cash flow data that may contain information value for security markets. Recent innovation in earnings response models are used to test the robustness of the results and provide further insights into the time series properties of cash flow numbers. The findings indicate that the disaggregation of cash flow as required under FRS1 contains information beyond aggregate cash flow but that the required disaggregation is not optimal from an information standpoint. There is little evidence of any incremental information value of cash flow per share over cash flow numbers.
Predicting Stock Returns Using Financial Statement Information
Authors: Setiono Strong Bambang, Norman
Published: November 2003

We examine the profitability of the Ou and Penman (1989a) Pr trading strategy and the Holthausen and Larcker (1992) Prob trading strategy over the period 1980–1992 in the UK. This is a test of whether an investor can earn abnormal returns by exploiting fundamental accounting data. We employ alternative abnormal return metrics and research designs to control for risk. Using a UK dataset offers an independent test because the UK differs from the US in its formal and informal financial reporting environment, its structure of share ownership, and the behaviour of its economy over the study period. We find consistent evidence that an investor could have used a summary measure of financial statement information to predict future abnormal returns by indirectly predicting one‐year‐ahead earnings changes, but only weak and inconsistent evidence that an investor could have used a summary measure of financial statement information to predict one‐year‐ahead stock returns directly. We offer some thoughts on the reasons for these different results.
Sex differences in L2 vocabulary learning strategies
Authors: Catalán Rosa María Jiménez
Published: November 2003

This article reports the results of a descriptive study on sex differences in the use of a second language. A questionnaire was administered to 581 Spanish‐speaking students learning Basque and English as L2 (279 males and 302 females) in order to answer these questions: Do male and female second language learners differ in (1) the number and (2) the range of vocabulary strategies they use? The results show that they differ significantly in the number of strategies used. Regarding the range of vocabulary strategies, 8 out of the 10 most frequent strategies are shared by males and females. However, a close analysis of the data also reveals differences, such as females’ greater use of formal rule strategies, input elicitation strategies, rehearsal strategies and planning strategies, and males’ greater use of image vocabulary learning strategies. In addition, the females’ total strategy usage percentages are higher than the males’, which points to either different perceptions of vocabulary learning behaviors or different patterns of vocabulary strategy usage for males and females.
Student language learning strategies across eight disciplines
Authors: Peacock Matthew , Ho Belinda
Published: November 2003

The research on which this article reports investigated the use of 50 common second language learning strategies by 1,006 EAP (English for Academic Purposes) students across eight disciplines – building, business, computing, engineering, English, maths, primary education, and science – in a university in Hong Kong. The study compared and contrasted strategy use across disciplines and also examined the relationships among strategy use, L2 proficiency, age, and gender. Initial data were collected through a standard questionnaire, Oxford's Strategy Inventory for Language Learning. In‐depth interviews were also conducted with 48 students to explore why they did or did not use certain strategies. A positive association was found between 27 strategies and proficiency. English students used the most strategies, and computing the fewest. Different deficiencies in strategy use were found in different disciplines, for example the very low use of metacognitive strategies by computing students. Differences were also found by age and by gender: older students were strong in affective and social areas, and females in the use of memory and metacognitive strategies. Conclusions are that EAP teachers need to be aware of possibly sharp disciplinary differences in strategy use and to apply discipline‐specific strategy training where appropriate.
Local Area Management and Planning (LAMP) in India
Authors: Datta S.
Published: November 2003

To assist decentralised planning, the Department of Science and Technology, Government of India has taken the initiative to develop a computer‐based spatial information system for planning and management of the natural resources at the district and sub‐district level. At present ten district level database centres called Natural Resources Data Management System (NRDMS) have been functioning in different geo‐environments in India.

The present paper discusses the experience of the Centre for Applied Systems Analysis in Development (CASAD). CASAD is involved in managing the NRDMS database centre at Bankura district and was associated with the development of DSS models in Kheda district. Finally, a few case studies on the use of Decision Support Systems (DSS) for decentralised decision making at the district level are discussed.
Infinite‐horizon Scheduling Algorithms for Optimal Search for Hidden Objects
Authors: Levner Eugene
Published: November 2003

This paper considers discrete search problems in which a decision‐maker has to find objects lost or hidden in a given set of locations so as to minimize the expected losses incurred. Given a chance to look for a hidden object in the same location infinitely many times, this type of problem, in contrast to standard scheduling problems, has an infinite sequence as its solution. Thus we are concerned to find an algorithm that yields an optimal solution, rather than the optimal sequence itself. Using combinatorial techniques, fast optimal algorithms for solving the problems are obtained, and optimality conditions are presented for search criteria, under which the local‐search algorithms yield the global optimum.
Information Systems Planning within Medium Environments: a Critique of Information Systems Growth Models
Authors: Doukidis Georgios I. , Mylonopoulos Nikolaos A. , Lybereas Panagiotis
Published: November 2003

Nolan's and Galliers' stages‐of‐IS‐growth models have been applied to companies of various sizes, styles and structures. The case studies in this paper have revealed some problems and difficulties related to the applicability of these models. We suggest that the causes are rooted in the different organisational cultures found in various businesses. This paper focuses on medium‐sized entrepreneurial firms and argues that these models are inadequate to deal with the managerial practices and organisational structures found in these specific cultural contexts. Some considerations of the reasons behind these peculiarities and on the direction to broaden the scope of such models are set forth. The upshot is that the concept of organisational culture should become central in the study of Information Systems growth.
Tabu Search within a Pivot and Complement Framework
Authors: Løkketangen Arne , Jörnsten Kurt , Storøy Sverre
Published: November 2003

The Pivot and Complement heuristic is a procedure that frequently finds feasible solutions for general 0–1 integer programs. We present a refinement of the heuristic based on Tabu Search techniques. Local search strategies for the search phase, as well as the improvement phase of the heuristic are presented.
The Possibilities of Community OR in a Third World Country
Authors: Ochoa Arias Alejandro E.
Published: November 2003

This paper shows a few possibilities for the application of Community OR in a Third World country based on experience in Venezuela. These possibilities are discussed in a framework of the relationship between the state and community organizations. Emphasis lies in showing that Community OR in Venezuela requires a deep critical commitment to emancipation in order to help community organizations develop in a rather hostile environment. Lastly, results in dealing with community organizations in Venezuela using the Interpretive Systemology approach are presented.
Partisan responses to Europe: Comparing Finnish and Swedish political parties
Authors: JOHANSSON KARL MAGNUS , RAUNIO TAPIO
Published: November 2003

Abstract. This article analyzes party responses to European integration in Finland andSweden.We argue that such responses are shaped by seven explanatory factors: basic ideology, public opinion, factionalism, leadership influence, party competition, transnational links, and the development of integration. Each factor can lead to a positive or a negative evaluation of the European Union. In the empirical analysis, the sample includes all parties represented in the respective national parliaments, and the research material consists of party documents, parliamentary votes, statements by leading party figures, public opinion surveys, direct observation and interviews. Party competition and leadership influence are the strongest factors in the Finnish case, while public opinion and factionalism are the strongest factors in Sweden. Issue avoidance combined with the secondary importance of the EU in party politics explain why parties have been relatively successful in containing internal factionalism and discord, especially in Finland.