bluuebunny/crossref_metadata_2025_split huggingface dataset:
Review and classification of structural controls on fluid flow during regional metamorphism
Authors: OLIVER N. H. S. 
Published: November 2003

Mechanisms for kilometre‐scale, open‐system fluid flow during regional metamorphism remain problematic. Debate also continues over the degree of fluid flow channellization during regional metamorphism, and the mechanisms for pervasive fluid flow at depth. The requirements for pervasive long‐distance fluid flow are an interconnected porosity and a large regional gradient in fluid pressure and hydraulic head (thermally or structurally controlled) that dominates over local perturbations in hydraulic head due to deformation. In contrast, dynamic or transient porosity interconnection and fluid flow accompanying deformation of heterogeneous rock suites should result in moderately to strongly channellized flow at a range of scales, of which there are many examples in the literature.Classification of fluid flow types based on scale and degree of equilibration between fluid and rock, wallrock permeability, and mode of fluid transport contributes to an understanding of key factors that control fluid flow. Closed‐system fluid behaviour, with restricted fluid flow in microcracks or cracks and limited fluid–rock interaction, occurs over a range of strains and crustal depths, but requires low permeabilities and/or small fluid fluxes. Long‐distance, open‐system fluid flow in channels is favoured in heterogeneous rocks at high strains, moderate (but variable) permeabilities, and moderate to high fluid fluxes. Long‐distance, broad, pervasive fluid flow during regional metamorphism requires that the rocks are not accumulating high strains and have high permeabilities, low permeability contrasts, and high fluid fluxes. The ideal situation for such fluid flow is in situations where the rocks are undergoing stress relaxation immediately after a major deformation phase. In the mid‐crust, fairly specific conditions are thus required for pervasive fluid flow. During active orogenesis, structurally controlled fluid flow (with focused open systems surrounding regions of closed‐system behaviour) predominates in most, but not all, regional metamorphic situations, at a range of scales.
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.
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.