bluuebunny/crossref_metadata_2025 huggingface dataset:
Distribution of fungal foliage and shoot pathogens in a natural Scots pine population in relation to environmental variables
Authors: Ranta Hanna , Saloniemi Irma
Published: April 2005

The development of fungal diseases within plant populations is simultaneously affected by spatially varying factors, which include environmental variables as well as characteristics of the host population itself. We studied the effects of such variation by investigating the relationships between several environmental factors and the occurrence and abundance of pathogenic fungi (Phacidium infestans L., Gremmeniella abietina (Lagerb.) Morelet, and Lophodermella sulcigena (Rostr.) Höhn) in a naturally regenerated, postfire population of Scots pine (Pinus sylvestris L.) saplings. The fieldwork was carried out in the pristine forest of Kostamuksha Strict Nature Reserve in the Karelian Republic, Russia. The microhabitat as well as the density and height of the saplings were factors that were related to the extent of damage caused by fungal diseases. However, the factors were correlated to the amounts of single pathogen species in different ways. Most obviously, microhabitat was related to the amount of G. abietina, while the amount of P. infestans was positively correlated with the increasing density of the stand. Lophodermella sulcigena was most abundant on tall saplings. Gremmeniella abietina occurred together with the other two fungi less frequently than would be expected from random occurrence, suggesting different ecological requirements or competitive exclusion. Fungal diseases caused considerable mortality and damage in the Scots pine population in question. We suggest that pathogenic fungi affecting shoots and foliage may affect the spatial distribution and regeneration dynamics of natural Scots pine populations.
Bryophyte community differences between edge and interior environments in temperate rain-forest fragments of coastal British Columbia
Authors: Baldwin Lyn K , Bradfield Gary E
Published: April 2005

The species richness, community composition, and abundance of bryophytes within taxonomic and functional groups were examined in relation to habitat conditions in forest edge and interior habitats of nine old-growth temperate rain-forest patches remaining after logging in the Nimpkish River Valley of Vancouver Island, British Columbia. Bryophytes were sampled at a fine scale using 0.1 m × 0.3 m microplots to examine responses of species abundance on the forest floor, downed logs, and tree bases and at a coarser scale using 10 m × 2 m belt transects to determine changes in patterns of species richness and distribution. Edge habitats, sampled to a depth of 45 m into the forest fragments, were characterized by greater windthrow disturbance. Within the edge zone, increases in the richness of clearing-affiliated functional groups were associated primarily with the location of windthrown trees and tip-up mounds, rather than with distance from the edge per se. Interior habitats had both greater abundance of old-growth-associated functional groups and total bryophyte cover. The extension of the edge zone to at least 45 m into remnant patches carries implications for minimum patch size requirements in the context of variable-retention logging of coastal temperate rain forests.
Invertebrate predation of postdispersal seeds and juvenile seedlings of black spruce (Picea mariana) in the boreal forest of eastern Canada
Authors: Côté Mathieu , Ferron Jean , Gagnon Réjean
Published: April 2005

We used an extensive vertebrate exclosure experiment to evaluate black spruce (Picea mariana (Mill.) B.S.P.) postdispersal seed and seedling predation by invertebrates in three boreal habitats of Eastern Canada: recent burn, sprucemoss, and lichen woodland. Between 9% and 19% of seeds were eaten by invertebrates. Seed predation was higher in recent burns than in sprucemoss and lichen woodlands. Abundance and diversity of potential invertebrate seed consumers sampled in pitfall traps also varied among habitat types. Among the invertebrate seed consumers sampled, Myrmica spp. (Hymenoptera: Formicidae) and Pterostichus adstrictus (Eschscholtz, 1823) (Coleoptera: Carabidae) were the most numerous; Formica spp. (Hymenoptera: Formicidae) and Pterostichus punctatissimus (Randall, 1838) (Coleoptera: Carabidae) were also present. Between 2% and 12% of juvenile black spruce seedlings were eaten by invertebrates. The most important seedling consumers were slugs (molluscs). Invertebrate predation of seeds and seedlings was highest (19% and 12%) in recent burns, indicating that invertebrate predation may significantly influence black spruce regeneration in these sites.
Dynamics of dead wood over 20 years in a New England oak forest
Authors: Wilson Brayton F , McComb Brenda C
Published: April 2005

Trees and snags with diameter at breast height (dbh) ≥5 cm were measured in 1983, 1993, and 2003 on 117 plots, each having an area of 200-m2, in an 80-year-old forest in western Massachusetts. In 2003 we measured dead stumps and coarse woody debris (CWD) with diameter ≥10 cm using the line intercept method. Decadal mortality rates were 9.4% and 9.0% per decade (7.1 and 5.0 m3·ha1, respectively). Mortality rates were highest (32%) in low-vigor suppressed trees. Snags with dbh > 10 cm occurred on 72% and 62% of plots, respectively, in 1983 and 2003. Snag volume decreased from 13.2 to 8.7 m3·ha1 over the 20-year period. From 1983 to 2003, 88% of a cohort of oak (Quercus spp.) snags, probably killed by gypsy moths (Lymantria dispar L.), had fallen. Decadal fall rates of snags averaged 61% and 66% (6.8 and 4.5 m3·ha1, respectively). CWD logs were measured on 55% of plots and averaged 10.1 m3·ha1. Stumps were on 62% of plots and averaged 0.7 m3·ha1. Seventy percent of stumps, but only 38% of logs, were in the two most decayed classes. Trees cut the previous decade contributed 6% of CWD logs measured. Few snags were cut (1.6 and 0.4 m3·ha1, respectively, in 19831993 and 19932003). Snag production and fall rates were higher than in other forests, but CWD volume was lower.
Fire frequency for the transitional mixedwood forest of Timiskaming, Quebec, Canada
Authors: Grenier Daniel J , Bergeron Yves , Kneeshaw Daniel , Gauthier Sylvie
Published: April 2005

Fire history was reconstructed for a 2500-km2 area at the interface between the boreal coniferous and northern hardwood forests of southwestern Quebec. The fire cycle, the time required for an area equal to the study site to burn once over, was described using a random sampling strategy that included dendrochronological techniques in conjunction with provincial and national government archival data. Physiographic elements were not found to spatially influence fire frequency; however, human land-use patterns were observed to significantly affect the fire frequency. A temporal shift in fire frequency was also detected, which coincided with the period of Euro-Canadian colonization and known extreme dry years for the study site. Additionally, a fire-free period was identified in the most recent times that could be associated with fire suppression and climate change. The estimated cycles (approx. 188314 years) for the southeastern section of the study area were thought to better represent the natural cycles for this transition zone as a result of less anthropogenic influence. The importance of gap-type dynamics becomes evident with the increased presence of old-growth forest, given the derived fire cycle estimations for the region. Even-aged management with short rotations, consequently, is questioned because fire cycle estimations suggest more complex harvest systems using an ecosystem management approach.
OPTIMAL PREVENTIVE-MAINTENANCE WARRANTY POLICIES FOR REPAIRABLE PRODUCTS WITH AGE-DEPENDENT MAINTENANCE COSTS
Authors: YEH RUEY HUEI , CHEN MING-YUH
Published: April 2005

This paper develops a mathematical model to derive the optimal preventive maintenance warranty (PMW) policy for repairable products with age-dependent maintenance costs. Under a PMW, any product failures are rectified by minimal repair, and additional preventive maintenance actions are carried out within the warranty period. When the costs for preventive maintenance and minimal repair are age-dependent, the optimal number of preventive maintenance actions, corresponding maintenance degrees, and the maintenance schedule for designing a PMW policy are derived here such that the expected total warranty cost is minimized. Under some reasonable conditions, we show that there exists a unique optimal PMW policy in which the product is maintained periodically with the same preventive maintenance degree. Using this property, an efficient algorithm is provided to search for the optimal policy. Some related models developed in the literature are discussed and these models are in fact special cases of the model proposed in this paper. Furthermore, when the life-time distribution of a product is Weibull, a closed-form expression of the optimal policy is obtained. Finally, the impact of providing preventive maintenance is evaluated through numerical examples.
SHORT RUNS MULTIVARIATE CONTROL CHART FOR PROCESS DISPERSION
Authors: KHOO MICHAEL B. C. , QUAH S. H. , LOW H. C. , CH'NG C. K.
Published: April 2005

The multivariate Hotelling's T2 control chart is designed to be used in a mass production for processes where data to estimate the mean vector and covariance matrix as well as the computation of control limits are available before a production run. Recent years have seen a trend in manufacturing industries to produce smaller lot sizes, a.k.a., low volume production which is a result of increased importance given to just-in-time (JIT) manufacturing techniques, synchronous manufacturing and the reduction of in-process inventory and costs. This new manufacturing environment is also referred to as short runs production or short runs. In a short runs environment, it is difficult or perhaps impossible to establish a reliable historical data set in setting valid control limits and in estimating process parameters due to the availability of insufficient data for a particular process because production runs are usually short and change frequently from one process to another. There is also a need to start charting at or very near the beginning of the run in such a case. Another problem encountered in a short runs production such as in job shops is that there are many different types of measurements so that many different control charts are needed. Standardized control charts that allow different statistics to be plotted on the same chart are extremely useful in short runs. Control charts with standard scale simplify the control charting process in a short runs environment. In this paper, we address the multivariate short runs problems for process dispersion based on individual measurements by presenting the required formulas so that the chart can be used from the start of production, whether or not prior information for estimating the chart's limit and its parameter is available. The proposed chart plots standardized statistics for multiple parts on the same chart. This paper extends the work of the authors in Ref. 13.
LIKELIHOOD RATIO BASED MULTI-ATTRIBUTE CONTROL CHART
Authors: GADRE M. P. , RATTIHALLI R. N.
Published: April 2005

In a production process, when quality of the product depends on more than one characteristic, 'Multivariate Quality Control' (MQC) techniques are efficiently used. Many MQC techniques have been developed to control the multivariate variable processes, but no much work has been reported to control the multivariate attribute processes.

In this article, to detect a change in the vector of fraction non-conforming, we develop 'Likelihood Ratio based Multi-Attribute Control Chart' (LR-MACC) using the exact joint distribution and the LR-test under multinomial setup. It is verified that, in some situations, LR-MACC is superior to the MNP chart proposed by Lu et al.7

When MACC gives a signal, the attributes responsible are not readily identifiable. Therefore, a procedure to detect the responsible attributes is also developed.
MINIMUM REDUNDANCY FEATURE SELECTION FROM MICROARRAY GENE EXPRESSION DATA
Authors: DING CHRIS , PENG HANCHUAN
Published: April 2005

How to selecting a small subset out of the thousands of genes in microarray data is important for accurate classification of phenotypes. Widely used methods typically rank genes according to their differential expressions among phenotypes and pick the top-ranked genes. We observe that feature sets so obtained have certain redundancy and study methods to minimize it. We propose a minimum redundancy — maximum relevance (MRMR) feature selection framework. Genes selected via MRMR provide a more balanced coverage of the space and capture broader characteristics of phenotypes. They lead to significantly improved class predictions in extensive experiments on 6 gene expression data sets: NCI, Lymphoma, Lung, Child Leukemia, Leukemia, and Colon. Improvements are observed consistently among 4 classification methods: Naïve Bayes, Linear discriminant analysis, Logistic regression, and Support vector machines.

Supplimentary: The top 60 MRMR genes for each of the datasets are listed in . More information related to MRMR methods can be found at .
COMPLEXITY AND APPROXIMABILITY OF DOUBLE DIGEST
Authors: CIELIEBAK MARK , EIDENBENZ STEPHAN , WOEGINGER GERHARD J.
Published: April 2005

We revisit the DOUBLE DIGEST problem, which occurs in sequencing of large DNA strings and consists of reconstructing the relative positions of cut sites from two different enzymes. We first show that DOUBLE DIGEST is strongly NP-complete, improving upon previous results that only showed weak NP-completeness. Even the (experimentally more meaningful) variation in which we disallow coincident cut sites turns out to be strongly NP-complete. In the second part, we model errors in data as they occur in real-life experiments: we propose several optimization variations of DOUBLE DIGEST that model partial cleavage errors. We then show that most of these variations are hard to approximate. In the third part, we investigate variations with the additional restriction that coincident cut sites are disallowed, and we show that it is NP-hard to even find feasible solutions in this case, thus making it impossible to guarantee any approximation ratio at all.
SYSTEMATIC VARIATION NORMALIZATION IN MICROARRAY DATA TO GET GENE EXPRESSION COMPARISON UNBIASED
Authors: CHOU JEFF W. , PAULES RICHARD S. , BUSHEL PIERRE R.
Published: April 2005

Normalization removes or minimizes the biases of systematic variation that exists in experimental data sets. This study presents a systematic variation normalization (SVN) procedure for removing systematic variation in two channel microarray gene expression data. Based on an analysis of how systematic variation contributes to variability in microarray data sets, our normalization procedure includes background subtraction determined from the distribution of pixel intensity values from each data acquisition channel and log conversion, linear or non-linear regression, restoration or transformation, and multiarray normalization. In the case when a non-linear regression is required, an empirical polynomial approximation approach is used. Either the high terminated points or their averaged values in the distributions of the pixel intensity values observed in control channels may be used for rescaling multiarray datasets. These pre-processing steps remove systematic variation in the data attributable to variability in microarray slides, assay-batches, the array process, or experimenters. Biologically meaningful comparisons of gene expression patterns between control and test channels or among multiple arrays are therefore unbiased using normalized but not unnormalized datasets.
AN ANCOVA APPROACH TO NORMALIZE MICROARRAY DATA, AND ITS PERFORMANCE TO EXISTING METHODS
Authors: CHAN SHIH-HUANG , CHEN LI-JU , CHOW NAN-HWA , LIU HSIAO-SHENG
Published: April 2005

A microarray experiment includes many steps, and each one of them may include systematic variations. To have a sound analysis, the systematic bias must be identified and removed prior to the data being analyzed. Based on the M-A dependency observed by Dudoit et al. (2002), we suggest that, instead of using the lowess normalization, a new normalization method called ANCOVA be used for dealing with genes with replicates. Simulation studies have shown that the performance of the suggested ANCOVA method is superior to any of the available approaches with regards to the Fisher's Z score and concordance rate. We used a microarray data from bladder cancer to illustrate the application of our approach. The edge the ANCOVA method has over the existing normalization approaches is further confirmed through real-time PCR.
APPROXIMATE MATCHING OF STRUCTURED MOTIFS IN DNA SEQUENCES
Authors: EL-MABROUK NADIA , RAFFINOT MATHIEU , DUCHESNE JEAN-EUDES , LAJOIE MATHIEU , LUC NICOLAS
Published: April 2005

Several methods have been developed for identifying more or less complex RNA structures in a genome. All these methods are based on the search for conserved primary and secondary sub-structures. In this paper, we present a simple formal representation of a helix, which is a combination of sequence and folding constraints, as a constrained regular expression. This representation allows us to develop a well-founded algorithm that searches for all approximate matches of a helix in a genome. The algorithm is based on an alignment graph constructed from several copies of a pushdown automaton, arranged one on top of another. This is a first attempt to take advantage of the possibilities of pushdown automata in the context of approximate matching. The worst time complexity is O(krpn), where k is the error threshold, n the size of the genome, p the size of the secondary expression, and r its number of union symbols. We then extend the algorithm to search for pseudo-knots and secondary structures containing an arbitrary number of helices.
THREE-DIMENSIONAL DEFINITION OF LEAF MORPHOLOGICAL TRAITS OF ARABIDOPSIS IN SILICO PHENOTYPIC ANALYSIS
Authors: KAMINUMA ELI , HEIDA NAOHIKO , TSUMOTO YUKO , NAKAZAWA MIKI , GOTO NOBUHARU , KONAGAYA AKIHIKO , MATSUI MINAMI , TOYODA TETSURO
Published: April 2005

The detection of phenotypic alterations of mutants and variants is one of the bottlenecks that hinder systematic gene functional studies of the model plant Arabidopsis. In an earlier study, we have addressed this problem by proposing a novel methodology for phenome analysis based on in silico analysis of polygon models that are acquired by 3-dimensional (3D) measurement and which precisely reconstruct the actual plant shape. However, 3D quantitative descriptions of morphological traits are rare, whereas conventional 2D descriptions have already been studied but may lack the necessary precision. In this report, we focus on six major leaf morphological traits, which are commonly used in the current manual mutant screens, and propose new 3D quantitative definitions that describe these traits. In experiments to extract the traits, we found significant differences between two variants of Arabidopsis with respect to blade roundness and blade epinasty. Remarkably, the detected difference between variants in the blade roundness trait was undetectable when using conventional 2D descriptions. Thus, the result of the experiment indicates that the proposed definitions with 3D description may lead to new discoveries of phenotypic alteration in gene functional studies that would not be possible using conventional 2D descriptions.
AN OPTIMIZATION METHOD FOR THE IDENTIFICATION OF MINIMAL SETS OF DISCRIMINATING GENE MARKERS: APPLICATION TO CULTIVAR IDENTIFICATION IN WHEAT
Authors: GALE KEVIN , JIANG HOUYUAN , WESTCOTT MARK
Published: April 2005

A potentially large number of molecular markers are available for identifying genotypes in various species. For wheat, cultivar identity is an important determinant for end-use segregation and for payment of end-point royalties and grower premiums. A number of dominant DNA markers, that give either a positive or negative response, have been developed previously for wheat cultivar identification. This paper gives a method for identifying minimal marker sets for a given cultivar group, for example those grown in a specific geographical zone. It is based on an integer linear programming formulation of the problem, and can find all minimal marker sets for the group if required. The paper then describes the production of two software packages, GGDS and GGIP, that incorporate this methodology. Various practical issues are also discussed.

These packages enable the rapid selection of minimal marker sets for the efficient discrimination of any sample set where the marker responses of the samples are known. They are already being used by the Australian wheat industry.
CLUSTERING GENE EXPRESSION DATA WITH KERNEL PRINCIPAL COMPONENTS
Authors: LIU ZHENQIU , CHEN DECHANG , BENSMAIL HALIMA , XU YING
Published: April 2005

Kernel principal component analysis (KPCA) has been applied to data clustering and graphic cut in the last couple of years. This paper discusses the application of KPCA to microarray data clustering. A new algorithm based on KPCA and fuzzy C-means is proposed. Experiments with microarray data show that the proposed algorithms is in general superior to traditional algorithms.
Sedimentation in a humid, interior, extensional basin: the Cenozoic Li Basin, northern Thailand
Authors: Nichols Gary , Uttamo Wutti
Published: April 2005

Facies distributions in extensional basins are controlled by a combination of factors including local and regional tectonics, climate, hinterland characteristics and base-level changes. During the mid-Cenozoic, northern Thailand was a region in which active basin formation was occurring as a result of regional extension related to major strike-slip faults. It was also a time when the climate was relatively humid. The Li Basin is one of about 40 Cenozoic basins in northern Thailand that have a fill of continental facies, and it is also one of a number of basins that contain economic coal deposits. Analysis of the geographical and temporal distribution of facies in the Li Basin indicates that it had internal drainage fed by rivers that supplied water and sediment to extensive floodplain and lake environments. Variations in the sediment supply were an important control on the relative development of fluvial channel and muddy overbank facies during periods of high clastic input and peat swamp and lacustrine facies when clastic input was lower. Changes in palaeosol type and the occurrence of peat deposits indicate that there was a trend towards drier conditions through the period of deposition of the available sections (Late Oligocene to Miocene). The Li Basin succession provides an example of a small (500 km
2
) extensional basin formed in a humid climate with interior drainage and periods of low clastic sediment supply. These conditions resulted in an association of facies deposited in permanent lakes, peat swamps, wet and dry floodplains, fluvial channels and local alluvial fans. The relationships between depositional facies and tectonic, climatic and sediment supply controls established in this case study may be applicable to other rift and transtensional basins.
Combining ground penetrating radar surveys and optical dating to determine dune migration in Namibia
Authors: Bristow C.S. , Lancaster N. , Duller G.A.T.
Published: April 2005

Ground penetrating radar (GPR) profiles across a complex linear dune in the Namib Sand Sea have been used to image sets of cross-stratification and their bounding surfaces. A combination of radar facies analysis and radar stratigraphy has been used to interpret the radar profiles and define a relative chronology. Thick sets of cross-stratification indicate when the dune was most active, whereas thin sets of cross-stratification are interpreted to indicate the increased prevalence of wind reversals and lower rates of dune migration, with bounding surfaces formed during periods of stabilization, non-deposition or erosion. A drilling and dating campaign was designed on the basis of the dune stratigraphy as defined by the GPR survey. Sampling was targeted at large sets of cross-stratification formed when the dunes were most active, and avoiding bounding surfaces formed when the dune was stable or even eroded. The results from optical dating give ages between 0.34 ± 0.02 ka and 1.57 ± 0.07 ka, indicating a time-averaged dune migration rate of 0.12 m a
−1
over the past 1600 years.
Formation and emplacement of the Northland ophiolite, northern New Zealand: SW Pacific tectonic implications
Authors: Whattam Scott A. , Malpas John , Ali Jason R. , Lo Ching-Hua , Smith Ian E. M.
Published: April 2005

Petrological, geochemical, geochronological and palaeomagnetic data for rocks of the Northland ophiolite terrane of northern New Zealand suggest that it formed in a suprasubduction-zone setting between
c
. 29 and 26 Ma, at
c
. 35°S, close to its Late Oligocene obduction site. Cretaceous igneous rocks formerly considered to be part of the ophiolite probably represent the basement upon which the ophiolite was emplaced, and are probably part of the Mount Camel arc-related terrane. The ophiolite is believed to have been generated in the southeastern South Fiji Basin, close to a NW–SE-oriented transform fault located to the SW of the Vening Meinesz Fracture Zone, and was probably emplaced in response to the collision of the Hikurangi Plateau with eastern New Zealand at the end of the Oligocene. This collision would have involved a major adjustment on the transform fault, thereby allowing a portion of the upper-crustal section of the southern South Fiji Basin to be emplaced southwestward onto northern New Zealand as well as the coeval emplacement of the East Cape Allochthon to the south. Concomitant subduction of the lower crust–mantle section led to the initiation of arc volcanism that resulted in the Northland Lower Miocene volcanic–plutonic suite.
Jurassic evolution of the Arabian carbonate platform edge in the central Oman Mountains
Authors: Rousseau Mathieu , Dromart Gilles , Garcia Jean-Pierre , Atrops Francois , Guillocheau François
Published: April 2005

The Jurassic Sahtan Group exposed in northern Oman was deposited in shallow marine environments at the edge of the Arabian Platform facing the Neo-Tethys (Hamrat Duru Basin). The upper Sahtan Group is made up of a mixed siliciclastic–carbonate unit overlain by pure carbonate deposits, assigned to a Bathonian and Early Callovian age on the basis of brachiopods and foraminifers. These carbonate depositional systems were composed of outer oolitic shoals that underwent subaerial exposure, and a deeper, somewhat restricted, gently dipping shelf interior. Oolitic material was shed off the platform edge into the deep-sea depositional complex of the Guweyza Formation. The Sahtan Group is affected by an important thickness reduction towards northeastern Jabal Akhdar. The angular unconformity (0.2%) at the top of the Sahtan Group is shown to result from tilting and top truncation of genetic sequences. This unconformity is overlain by the Rayda Formation, a veneer that shows an onlap pattern including a gradual deepening upwards facies evolution. The minimal time span of the stratigraphic hiatus is Mid-Callovian–Kimmeridgian. Oxfordian and Kimmeridgian sequences were probably never deposited in this area because of lack of accommodation space and/or because of subaerial exposure. It is proposed herein that the unconformity was shaped by subaerial carbonate dissolution during a steady, tectonically driven exhumation of the platform edge. During the Tithonian, a major eustatic sea-level rise caused transgression of the Rayda Formation upon the platform edge and normal shelf marine conditions resumed in the eastern Arabian Peninsula.
Timing of Cadomian deformation and magmatism within La Hague, NW France
Authors: Inglis J.D. , Samson S.D. , D'Lemos R.S. , Miller B.V.
Published: April 2005

The La Hague peninsula, Normandy, NW France, contains the most northerly components of the Late Neoproterozoic Cadomian orogeny. U–Pb dates for single-grain and small multiple-grain zircon separates from carefully selected plutons provide geochronological constraints on the timing of deformation and magmatism within the region. The syntectonic Jardeheu quartz diorite and Omonville granodiorite were emplaced and contemporaneously deformed during the development of a greenschist-facies fabric, pervasive across the peninsula. U–Pb zircon dates of 610 ± 1 Ma for the Jardeheu quartz diorite and 608 ± 2 Ma for the Omonville granodiorite are similar to a previously reported sensitive high-resolution ion microprobe U–Pb date for metamorphism of the basement, and indicate that a regionally significant period of metamorphism and magmatism occurred between 620 and 608 Ma. An emplacement age of 573.9 +1.3/−0.9 Ma for the syntectonic Thiébot granodiorite places limits on the timing of deformation along the Thiébot Shear Zone. Zircons from the undeformed St Martin monzonite give a precise U–Pb age of 581.3 ± 1.1 Ma. The new dates point to reactivation of magmatism and localized greenschist-facies deformation between 582 and 573 Ma.
Two new Emsian (Early Devonian) U–Pb zircon ages from volcanic rocks of the Rhenish Massif (Germany): implications for the Devonian time scale
Authors: Kaufmann B. , Trapp E. , Mezger K. , Weddige K.
Published: April 2005

So far, only few biostratigraphically well-constrained isotopic ages constitute the geochronological framework of the Devonian period. To expand this sparse dataset, two new U–Pb isotope dilution–thermal ionization mass spectrometry (ID-TIMS) zircon ages were obtained from volcanic rocks of the Rhenish Massif (Germany). These rocks are interbedded in Emsian (Lower Devonian) marine sedimentary successions that are well documented by index fossils. Given that the U–Pb zircon data represent primary crystallization and eruption ages, they provide an important contribution to the Devonian time scale. The older sample, a stratiform volcaniclastic layer (Hans-Platte) is collected from Bundenbach (Hunsrück), the type locality of the Lower Emsian Hunsrück Slate. A cluster of five coherent single-zircon analyses obtained from this layer yielded a weighted mean
206
Pb/
238
U age of 407.7 ± 0.7 Ma, which is regarded as the time of eruption of the pyroclastic rock. Biostratigraphically, the layer can be assigned to the upper part of the
Polygnathus excavatus
conodont zone. The younger U–Pb age was obtained from the Global Stratotype Section and Stratigraphic Point section at Wetteldorf (Eifel), where the K-bentonite ‘Hercules I’ is intercalated 13 m below the Lower–Middle Devonian boundary in the uppermost part of the
Polygnathus costatus patulus
conodont zone. Some of the 19 single-zircon analyses obtained from this bentonite appear to document significant influences of inheritance. The 13 youngest points are, however, concordant and form an elongated cluster along concordia with
206
Pb/
238
U ages between 392.2 and 407.7 Ma. Given the (risky) assumption that this age scattering is exclusively caused by varying amounts of inheritance, the youngest point of this cluster represents the analysis with the least or no inheritance. In this case, its
206
Pb/
238
U age of 392.2 ± 1.5 Ma should approach the eruptional age of the bentonite. The ages presented here in combination with U–Pb ID-TIMS zircon and monazite ages from other workers allow a recalibration of the early Emsian to early Eifelian interval of the Devonian time scale. The result is a duration of the Emsian stage (excluding the basal Emsian
P. kitabicus
conodont zone) of more than 17.2 Ma and an Emsian–Eifelian (= Early–Middle Devonian) boundary age of 391.8 ± 0.4 Ma.
Transcurrent shearing, granite sheeting and the incremental construction of the tabular 3.1 Ga Mpuluzi batholith, Barberton granite–greenstone terrane, South Africa
Authors: Westraat JanusD. , Kisters AlexanderF.M. , Poujol Marc , Stevens Gary
Published: April 2005

Structural, petrographic and geochronological studies show that the tabular 3.1 Ga Mpuluzi batholith in the Barberton granite–gneiss terrane in South Africa was emplaced via a combination of external and internal processes. External structural controls are indicated by systematic variations in intrusive relationships and strain along the margins of the Mpuluzi batholith and are consistent with an emplacement of the granite in a dilational jog within a NE–ENE-trending system of dextral transcurrent synmagmatic shear zones. Internally, the Mpuluzi batholith is essentially made up of granite sheets. The structurally higher parts of the granite are made up of shallowly dipping sheets that are underlain by an anastomosing network of steeply dipping, variably deformed dykes and sheets. These granite sheets at lower structural levels intruded either into the actively deforming shear zones or into extensional sectors between and along the bounding shear zones. Multiple intrusive relationships and geochronological evidence suggests that granite sheeting and the assembly of the pluton occurred over a period of 3–13 Ma. The spatial and temporal relationship between deformation and magma emplacement reflects episodes of incremental dilation related to deformation along the bounding shear zones and granite sheeting. The transition to the mainly subhorizontal granite sheets at higher structural levels of the tabular Mpuluzi batholith indicates the intrusion of the granites during subhorizontal regional shortening, where the reorientation of the minimum normal stress to vertical attitudes at the shallow levels of emplacement allowed for vertical dilation and subhorizontal emplacement of the granite sheets.
Tectonics of the Pliocene Homs basalts (Syria) and implications for the Dead Sea Fault Zone activity
Authors: Chorowicz J. , Dhont D. , Ammar O. , Rukieh M. , Bilal A.
Published: April 2005

Timing of activity along the Yammuneh segment (Lebanon–Syria) of the Dead Sea Fault Zone and its northward continuation is still a subject of controversy. Our field structural analysis and observations on radar, Landsat and digital elevation model imagery of the Homs region (Syria) are of concern for Plio-Quaternary tectonics of the whole northern part of the Dead Sea Fault Zone. We show in this paper that the northern Dead Sea Fault Zone has remained active since the onset of the Homs basalts at
c
. 6 Ma. Continuing movement in Recent times is indicated by the occurrence of Quaternary pull-apart structures and offset of active ravines along the fault. The Homs basalts are related to the distinct oval-shaped Shin volcanic edifice, of which the long axis trends NW. The volcano was fed through NW-striking tension fractures, which now form dykes and volcanic ridges. These patterns are consistent with a NE–SW extension that occurred
c
. 6 Ma ago. The northwestern end of the Shin volcano is left-laterally displaced
c
. 20 km, yielding a
c
. 3.3 mm a
−1
mean rate of relative movement between the Arabian and African plates. In the northern part of the Dead Sea Fault Zone, the overall trace of the main active Dead Sea Fault Zone is not a single transform but forms an irregular plate boundary composed of transform fault and collision belt segments. Fine-grained mylonite developed in the fault corridor may have favoured aseismic deformation in the Shin volcano area.
Separation of Palaeogene and Neogene uplift on Nuussuaq, West Greenland
Authors: Japsen Peter , Green Paul F. , Chalmers James A.
Published: April 2005

The geological record exposed on Nuussuaq, central West Greenland, shows that uplift in the Palaeocene, probably caused by impact of the Iceland plume head, was followed by kilometre-scale subsidence. Analysis of apatite fission-track and vitrinite-reflectance data from borehole samples down to 3 km depth reveals that the samples cooled from maximum palaeotemperatures between 40 and 30 Ma followed by two further cooling episodes beginning in the intervals 11–10 and 7–2 Ma. When the first cooling episode began, the samples from the neighbouring Gro-3 and Gane-1 boreholes were buried 1500–2000 m deeper than at the present day, and the palaeogeothermal gradient was 40–48 °C km
−1
. It is not clear whether this cooling involved exhumation or if it was due solely to reduction in heat flow and a drop in surface temperature. The two later episodes definitely involved exhumation because by then the palaeogeothermal gradient had declined to a value close to the assumed present value of 30 °C km
−1
, which agrees with estimates from offshore wells. The most recent cooling episode corresponds to the incision of the present-day relief (
c
. 1100 m) below the summits around the two boreholes. We conclude that the present-day high mountains of West Greenland were not uplifted during the Palaeogene, but are erosional remnants of a landmass uplifted during the Neogene.
A re-evaluation of a Laxfordian terrane boundary in the Lewisian Complex of South Harris, NW Scotland
Authors: Mason A.J. , Brewer T.S.
Published: April 2005

The recent reinterpretation of the Lewisian Complex as a series of amalgamated terranes represents a significant advance in our understanding of these rocks. However, on the Outer Hebrides, a key observation that a supposed post-1675 Ma terrane boundary is based on is flawed. Specifically, on South Harris a group of
c
. 1675 Ma granite pegmatites has previously been described as occurring only to the NE of, and terminating abruptly within, a supposed terrane-bounding shear zone (the Langavat Shear Zone), which thus post-dates the pegmatites. New mapping indicates that granite pegmatites occur on both sides of, and throughout the Langavat Shear Zone, and that within most of this shear zone the pegmatites are not strongly deformed, inconsistent with them predating this shear zone. Furthermore, new U–Pb geochronological data suggest that the pegmatites SW of the supposed boundary were also intruded around 1675 Ma, similar to those in the NE, and supporting the field evidence that the pegmatites continue through the Langavat Shear Zone without interruption. Two phases of post-pegmatite deformation are identified, but these relate to relatively minor reactivation of the Langavat Shear Zone, not the initiation of this major shear zone, which predates the pegmatites.
Inhibition of transient lower esophageal sphincter relaxations by electrical acupoint stimulation
Authors: Zou Duowu , Chen Wei Hao , Iwakiri Katsuhiko , Rigda Rachael , Tippett Marcus , Holloway Richard H.
Published: April 2005

Acupuncture has been shown to modulate visceral sensation and function. Traditionally, stimulation at the Neiguan (pericardial meridian) has been used to treat upper gastrointestinal symptoms. Some of the effects of acupuncture may be mediated through release of endogenous opioids and are reversed by naloxone. Gastric distension is the major trigger for transient lower esophageal sphincter (LES) relaxations (TLESRs). The aim of this study was to investigate the effect of electric stimulation at the Neiguan and naloxone on the TLESRs. In 14 healthy volunteers, electrical acupoint stimulation was applied at the Neiguan and a sham point on the hip in randomized order on the same day. In 12 healthy volunteers, the effects of naloxone (80 μg/kg iv bolus injection) and saline on electrical acupoint stimulation were compared on separate days at least 1 wk apart. Esophageal motility was measured during distension of the proximal stomach with 500 ml of air using a barostat balloon. Electric acupoint stimulation at the Neiguan decreased the rate of TLESRs by ∼40% from a median of 6/h to 3.5/h ( P < 0.02). Acupoint stimulation had no effect on basal LES pressure, the residual LES pressure during TLESRs, the duration of TLESRs, or gastrointestinal symptoms of fullness, bloating, discomfort, or nausea. The effect of acupoint stimulation was not inhibited by naloxone. Electric acupoint stimulation at the Neiguan significantly inhibits the frequency of TLESRs in response to gastric distention in healthy subjects. This effect does not appear to be mediated through μ-opioid receptors.
Modulation of electroneutral Na transport in sheep rumen epithelium by luminal ammonia
Authors: Abdoun Khalid , Stumpff Friederike , Wolf Katarina , Martens Holger
Published: April 2005

Ammonia is an abundant fermentation product in the forestomachs of ruminants and the intestine of other species. Uptake as NH3 or NH4+ should modulate cytosolic pH and sodium-proton exchange via Na+/H+ exchanger (NHE). Transport rates of Na+, NH4+, and NH3 across the isolated rumen epithelium were studied at various luminal ammonia concentrations and pH values using the Ussing chamber method. The patch-clamp technique was used to identify an uptake route for NH4+. The data show that luminal ammonia inhibits electroneutral Na transport at pH 7.4 and abolishes it at 30 mM ( P < 0.05). In contrast, at pH 6.4, ammonia stimulates Na transport ( P < 0.05). Flux data reveal that at pH 6.4, ∼70% of ammonia is absorbed in the form of NH4+, whereas at pH 7.4, uptake of NH3 exceeds that of NH4+ by a factor of approximately four. The patch-clamp data show a quinidine-sensitive permeability for NH4+ and K+ but not Na+. Conductance was 135 ± 12 pS in symmetrical NH4Cl solution (130 mM). Permeability was modulated by the concentration of permeant ions, with PK > PNH4 at high and PNH4 > PK at lower external concentrations. Joint application of both ions led to anomalous mole fraction effects. In conclusion, the luminal pH determines the predominant form of ammonia absorption from the rumen and the effect of ammonia on electroneutral Na transport. Protons that enter the cytosol through potassium channels in the form of NH4+ stimulate and nonionic diffusion of NH3 blocks NHE, thus contributing to sodium transport and regulation of pH.
Differentiation-dependent activation of the human intestinal alkaline phosphatase promoter by HNF-4 in intestinal cells
Authors: Olsen Line , Bressendorff Simon , Troelsen Jesper T. , Olsen Jorgen
Published: April 2005

The intestinal alkaline phosphatase gene ( ALPI) encodes a digestive brush-border enzyme, which is highly upregulated during small intestinal epithelial cell differentiation. To identify new putative promoter motifs responsible for the regulation of ALPI expression during differentiation of the enterocytes, we have conducted a computer-assisted cis-element search of the proximal human ALPI promoter sequence. A putative recognition site for the transcription factor hepatocyte nuclear factor (HNF)-4 was predicted at the positions from −94 to −82 in relation to the translational start site. The ability of HNF-4α to stimulate the expression from the ALPI promoter was investigated in the nonintestinal Hela cell line. Cotransfection with an HNF-4α expression vector demonstrated a direct activation of the ALPI promoter through this −94 to −82 element. EMSA showed that HNF-4α from nuclear extracts of differentiated intestinal epithelial cells (Caco-2) bound with high affinity to the predicted HNF-4 binding site. A 521 bp promoter fragment containing the HNF-4 binding site demonstrated a differentiation-dependent increase in promoter activity in Caco-2 cells. The presence of the HNF-4 binding site was necessary for this increase to occur.
rhVEGF treatment preserves pulmonary vascular reactivity and structure in an experimental model of pulmonary hypertension in fetal sheep
Authors: Grover Theresa R. , Parker Thomas A. , Markham Neil E. , Abman Steven H.
Published: April 2005

We have previously shown that lung VEGF expression is decreased in a fetal lamb model of PPHN and that VEGF165 inhibition causes severe pulmonary hypertension in fetal lambs. Therefore, we hypothesized that treatment with rhVEGF165 would preserve endothelium-dependent vasodilation and reduce the severity of pulmonary vascular remodeling in an experimental model of PPHN. We studied the effects of daily intrapulmonary infusions of rhVEGF after partial ligation of the ductus arteriosus (DA). We performed surgery in 24 late-gestation fetal lambs and placed catheters in the main pulmonary artery, left atrium, and aorta for pressure measurements and in the left pulmonary artery for drug infusions. A pressure transducer was placed around the LPA to measure blood flow to the left lung (Qp), and the DA was surgically constricted to induce pulmonary hypertension. rhVEGF165 or vehicle was infused for 7 or 14 days. ACh or 8-BrcGMP was infused on days 2 and 13 to assess endothelium-dependent and -independent vasodilation, respectively. ACh-induced vasodilation was reduced in PPHN lambs after 14 days (change in Qp from baseline, 106% vs. 11%). In contrast, the response to ACh was preserved in lambs treated with rhVEGF (change in Qp, 94% vs. 90%). Pulmonary vasodilation to 8-BrcGMP was not altered in PPHN lambs or enhanced by VEGF treatment. rhVEGF treatment increased expression of lung eNOS protein and decreased pulmonary artery wall thickness by 34% vs. PPHN lambs. We conclude that VEGF165 preserves endothelium-dependent vasodilation, upregulates eNOS expression, and reduces the severity of pulmonary vascular remodeling in experimental PPHN.
Early effects of mechanical ventilation on isotonic contractile properties and MAF-box gene expression in the diaphragm
Authors: Zhu Ercheng , Sassoon Catherine S. H. , Nelson Renee , Pham H. Tony , Zhu Lei , Baker Michael J. , Caiozzo Vincent J.
Published: April 2005

This study aimed to determine the time-dependent effects of diaphragmatic inactivity on its maximum shortening velocity ( Vmax) and the muscle atrophy F-box (MAF-box, atrogin-1) gene expression during controlled mechanical ventilation (CMV). Twenty-four New Zealand White rabbits were grouped into 1 day, 2 days, and 3 days of CMV and controls in equal numbers. The in vitro isotonic contractile properties of the diaphragm were determined. In addition, myosin heavy chain protein and mRNA, myosin light chain, MAF-box mRNA, and volume density of abnormal myofibrils were measured. Tetanic force decreased, and Vmaxincreased from control of 6.4 to 6.6, 7.7, and 8.1 muscle lengths per second after 1, 2, and 3 days of CMV, respectively ( P < 0.02). The increased Vmaxcompensated for the decreased tetanic force; consequently, compared with the controls, maximum power output was unchanged after 3 days of CMV. Vmaxcorrelated with the volume density of abnormal myofibrils [ y = 0.1 x + 5.7 ( r = 0.87, P < 0.01)]. In the diaphragm, MAF-box was overexpressed (355% of control) after 1 day of CMV, before the evidence of structural myofibril disarray. In conclusion, CMV produced a time-dependent increase in Vmaxthat was associated with the degree of myofibrillar disarray and independent of changes in myosin isoform expression. Furthermore, CMV produced an increase in MAF-box mRNA levels that may be partially or completely responsible for the degree of myofibrillar disarray resulting from CMV.