bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Interaction between Projection Neuron Precursors and Invading Interneurons via Stromal-Derived Factor 1 (CXCL12)/CXCR4 Signaling in the Cortical Subventricular Zone/Intermediate Zone
Authors: Tiveron Marie-Catherine , Rossel Mireille , Moepps Barbara , Zhang Yong Li , Seidenfaden Ralph , Favor Jack , König Norbert , Cremer Harold
Published: December 2006

Most cortical interneurons are generated in the subpallial ganglionic eminences and migrate tangentially to their final destinations in the neocortex. Within the cortex, interneurons follow mainly stereotype routes in the subventricular zone/intermediate zone (SVZ/IZ) and in the marginal zone. It has been suggested that interactions between invading interneurons and locally generated projection neurons are implicated in the temporal and spatial regulation of the invasion process. However, so far experimental evidence for such interactions is lacking.

We show here that the chemokine stromal-derived factor 1 (SDF-1; CXCL12) is expressed in the main invasion route for cortical interneurons in the SVZ/IZ. Most SDF-1-positive cells are proliferating and express the homeodomain transcription factors Cux1 and Cux2. Using MASH-1 mutant mice in concert with the interneuron marker DLX, we exclude that interneurons themselves produce the chemokine in an autocrine manner. We conclude that the SDF-1-expressing cell population represents the precursors of projection neurons during their transition and amplification in the SVZ/IZ. Using mice lacking the SDF-1 receptor CXCR4 or Pax6, we demonstrate that SDF-1 expression in the cortical SVZ/IZ is essential for recognition of this pathway by interneurons. These results represent the first evidence for a molecular interaction between precursors of projection neurons and invading interneurons during corticogenesis.
Brain-Derived Neurotrophic Factor Participates in Determination of Neuronal Laminar Fate in the Developing Mouse Cerebral Cortex
Authors: Fukumitsu Hidefumi , Ohtsuka Masanari , Murai Rina , Nakamura Hiroyuki , Itoh Kazuo , Furukawa Shoei
Published: December 2006

Lamina formation in the developing cerebral cortex requires precisely regulated generation and migration of the cortical progenitor cells. To test the possible involvement of brain-derived neurotrophic factor (BDNF) in the formation of the cortical lamina, we investigated the effects of BDNF protein and anti-BDNF antibody separately administered into the telencephalic ventricular space of 13.5-d-old mouse embryos. BDNF altered the position, gene-expression properties, and projections of neurons otherwise destined for layer IV to those of neurons for the deeper layers, V and VI, of the cerebral cortex, whereas anti-BDNF antibody changed some of those of neurons of upper layers II/III. Additional analysis revealed that BDNF altered the laminar fate of neurons only if their parent progenitor cells were exposed to it at approximately S-phase and that it hastened the timing of the withdrawal of their daughter neurons from the ventricular proliferating pool by accelerating the completion of S-phase, downregulation of the Pax6 (paired box gene 6) expression, an essential transcription factor for generation of the upper layer neurons, and interkinetic nuclear migration of cortical progenitors in the ventricular zone. These observations suggest that BDNF participates in the processes forming the neuronal laminas in the developing cerebral cortex. BDNF can therefore be counted as one of the key extrinsic factors that regulate the laminar fate of cortical neurons.
The Fate of Old Memories after Medial Temporal Lobe Damage
Authors: Bayley Peter J. , Hopkins Ramona O. , Squire Larry R.
Published: December 2006

Damage to the hippocampal region and related medial temporal lobe structures (perirhinal, entorhinal, and parahippocampal cortices) impairs new learning (anterograde amnesia) as well as memory for information that was acquired before the damage occurred (retrograde amnesia). We assessed retrograde amnesia with the Autobiographical Memory Interview (AMI) and with a news events test in six patients with damage limited primarily to the hippocampal region (H group) and two patients with large medial temporal lobe lesions (MTL group). On the news event test, the H group exhibited temporally limited retrograde amnesia covering ∼5 years. On the same test, the MTL group exhibited an extensive retrograde amnesia covering decades. Nevertheless, performance was relatively spared for very remote time periods. On the AMI, all patients had intact remote autobiographical memory. Because our patients with hippocampal lesions, as well as our patients with large MTL lesions, performed normally on the AMI, patients who perform poorly on the same test presumably have damage beyond the hippocampus and related structures in the medial temporal lobe. The findings emphasize the difference in the extent of retrograde amnesia associated with hippocampal lesions and large MTL lesions.
Collapsin Response Mediator Protein 1 Mediates Reelin Signaling in Cortical Neuronal Migration
Authors: Yamashita Naoya , Uchida Yutaka , Ohshima Toshio , Hirai Syu-ichi , Nakamura Fumio , Taniguchi Masahiko , Mikoshiba Katsuhiko , Honnorat Jérôme , Kolattukudy Pappachan , Thomasset Nicole , Takei Kohtaro , Takahashi Takuya , Goshima Yoshio
Published: December 2006

Collapsin response mediator protein 1 (CRMP1) is one of the CRMP family members that mediates signal transduction of axon guidance molecules. Here, we show evidence that CRMP1 is involved in Reelin (Reln) signaling to regulate neuronal migration in the cerebral cortex. Incrmp1−/−mice, radial migration of cortical neurons was retarded. This phenotype was not observed in thesema3A−/−andcrmp1+/−;sema3A+/−cortices. However, CRMP1 was colocalized with disabled-1 (Dab1), an adaptor protein in Reln signaling. In theRelnrl/rlcortex, CRMP1 and Dab1 were expressed at a higher level, yet tyrosine phosphorylated at a lower level. Loss ofcrmp1in adab1heterozygous background led to the disruption of hippocampal lamination, a Reeler-like phenotype. In addition to axon guidance, CRMP1 regulates neuronal migration by mediating Reln signaling.
An Essential Role for the Integrin-Linked Kinase–Glycogen Synthase Kinase-3β Pathway during Dendrite Initiation and Growth
Authors: Naska Sibel , Park Katya J. , Hannigan Gregory E. , Dedhar Shoukat , Miller Freda D. , Kaplan David R.
Published: December 2006

Multiple cues, including growth factors and circuit activity, signal to regulate the initiation and growth of mammalian dendrites. In this study, we have asked how these environmental cues regulate dendrite formation, and in particular, whether dendrite initiation and growth requires integrin-linked kinase (ILK) or its downstream effector, glycogen synthase kinase-3β (GSK-3β). In cultured sympathetic neurons, NGF and neuronal depolarization activated ILK and promoted dendrite initiation and growth, and inhibition of ILK (either pharmacologically, with a dominant-negative form of ILK, or by genetic knockdown) reduced depolarization-induced dendrite formation. In sympathetic neurons, ILK phosphorylated and inhibited GSK-3β, and inhibition of GSK-3β (either pharmacologically, with dominant-negative GSK-3β, or by genetic knockdown) caused robust dendrite initiation. GSK-3β inhibition also caused dendrite initiation in cultured cortical neurons and growth of hippocampal neurons in slice cultures. GSK-3β functioned downstream of ILK to regulate dendrite formation, because inhibition of GSK-3β promoted dendrite initiation even when ILK was simultaneously inhibited. Moreover, GSK-3β promoted dendrite formation in sympathetic neurons by regulating the activity of a key dendrite formation effector, the MAP (microtubule-associated protein) kinase kinase (MEK)–extracellular signal-regulated protein kinase (ERK) pathway. Specifically, inhibition of GSK-3β led to increased ERK phosphorylation, and inhibition of MEK completely blocked the effects of GSK-3β inhibition on dendrite initiation and growth. Thus, the ILK–GSK-3β pathway plays a key role in regulating dendrite formation in developing mammalian neurons.
Subcutaneous Nogo Receptor Removes Brain Amyloid-β and Improves Spatial Memory in Alzheimer's Transgenic Mice
Authors: Park James H. , Widi Gabriel A. , Gimbel David A. , Harel Noam Y. , Lee Daniel H. S. , Strittmatter Stephen M.
Published: December 2006

The production and aggregation of cerebral amyloid-β (Aβ) peptide are thought to play a causal role in Alzheimer's disease (AD). Previously, we found that the Nogo-66 receptor (NgR) interacts physically with both Aβ and the amyloid precursor protein (APP). The inverse correlation of Aβ levels with NgR levels within the brain may reflect regulation of Aβ production and/or Aβ clearance. Here, we assess the potential therapeutic benefit of peripheral NgR-mediated Aβ clearance in APPswe/PSEN-1ΔE9 transgenic mice. Through site-directed mutagenesis, we demonstrate that the central 15–28 aa of Aβ associate with specific surface-accessible patches on the leucine-rich repeat concave side of the solenoid structure of NgR. In transgenic mice, subcutaneous NgR(310)ecto-Fc treatment reduces brain Aβ plaque load while increasing the relative levels of serum Aβ. These changes in Aβ are correlated with improved spatial memory in the radial arm water maze. The benefits of peripheral NgR administration are evident when therapy is initiated after disease onset. Thus, the peripheral association of NgR(310)ecto-Fc with central Aβ residues provides an effective therapeutic approach for AD.
Connecdenn, A Novel DENN Domain-Containing Protein of Neuronal Clathrin-Coated Vesicles Functioning in Synaptic Vesicle Endocytosis
Authors: Allaire Patrick D. , Ritter Brigitte , Thomas Sebastien , Burman Jonathon L. , Denisov Alexei Yu. , Legendre-Guillemin Valerie , Harper Scott Q. , Davidson Beverly L. , Gehring Kalle , McPherson Peter S.
Published: December 2006

Clathrin-coated vesicles (CCVs) are responsible for the endocytosis of multiple cargo, including synaptic vesicle membranes. We now describe a new CCV protein, termed connecdenn, that contains an N-terminal DENN (differentially expressed in neoplastic versus normal cells) domain, a poorly characterized protein module found in multiple proteins of unrelated function and a C-terminal peptide motif domain harboring three distinct motifs for binding the α-ear of the clathrin adaptor protein 2 (AP-2). Connecdenn coimmunoprecipitates and partially colocalizes with AP-2, and nuclear magnetic resonance and peptide competition studies reveal that all three α-ear-binding motifs contribute to AP-2 interactions. In addition, connecdenn contains multiple Src homology 3 (SH3) domain-binding motifs and coimmunoprecipitates with the synaptic SH3 domain proteins intersectin and endophilin A1. Interestingly, connecdenn is enriched on neuronal CCVs and is present in the presynaptic compartment of neurons. Moreover, connecdenn has a uniquely stable association with CCV membranes because it resists extraction with Tris and high-salt buffers, unlike most other CCV proteins, but it is not detected on purified synaptic vesicles. Together, these observations suggest that connecdenn functions on the endocytic limb of the synaptic vesicle cycle. Accordingly, disruption of connecdenn interactions with its binding partners through overexpression of the C-terminal peptide motif domain or knock down of connecdenn through lentiviral delivery of small hairpin RNA both lead to defects in synaptic vesicle endocytosis in cultured hippocampal neurons. Thus, we identified connecdenn as a component of the endocytic machinery functioning in synaptic vesicle endocytosis, providing the first evidence of a role for a DENN domain-containing protein in endocytosis.
Time to Leave (Le Temps qui reste)
Authors: Wilson Emma
Published: December 2006

ABSTRACT Following Under the Sand (2000), François Ozon's Time to Leave (2005) is the second film in a proposed trilogy about mourning. This essay explores the film's meditation on a dying gay photographer's last days, discussing how it seems to blur the distinctions between dream and reality, memory and fantasy, love and trauma.
When the Levees Broke: A Requiem in Four Acts
Authors: Callenbach Ernest
Published: December 2006

ABSTRACT Spike Lee's documentary about the Hurricane Katrina disaster in New Orleans is a harrowing assemblage of personal testimonies from city residents and an indictment of the response from government agencies. This review analyzes When the Levees Broke as a documentary film and a powerful testimony to a catastrophe.
The Savior, the Woman, and the Head of the Dragon in the Caput Masses and Motet
Authors: ROBERTSON ANNE WALTERS
Published: December 2006

God's dramatic curse of Adam, Eve, and the serpent, as recorded in Genesis 3:14–15, contains a theological ambiguity that played out in the visual arts, literature, and, as this article contends, music of the fifteenth and sixteenth centuries. Translations of this passage leave in doubt whether a male, a female, or both, will defeat sin by crushing Satan's head (“caput”). This issue lies at the heart of the three Caput masses by an anonymous Englishman, Johannes Ockeghem, and Jacob Obrecht, and the Caput Motet for the Virgin by Richard Hygons from the Eton Choirbook.

Fifteenth-century discussions of the roles of Christ and Mary in confronting sin, often called the “head of the dragon,” help unravel the meaning of these works. The Caput masses are Christ-focused and emphasize the Savior or one of his surrogates suppressing the beast's head, as seen in illumination, rubric, and canon found in the masses. Folklorically based rituals and concepts of liturgical time are similarly built around the idea of the temporary reign of the Devil, who is ultimately trodden down by Christ. Hygons's motet appears after celebration of the Immaculate Conception was authorized in the late fifteenth century. This feast proclaimed Mary's conquest of sin through her own trampling on the dragon; the motet stresses Marian elements of the Caput theology, especially the contrast between the Virgin's spotlessness and Eve's corruption. Features of the Caput tradition mirror topics discussed in astrological and astronomical treatises and suggest that the composer of the original Caput Mass may also have been an astronomer. The disappearance of the Caput tradition signals its lasting influence through its progeny, which rise up in yet another renowned family of polyphonic masses.

Together, the Caput masses and motet encompass the multifaceted doctrine of Redemption from the late middle ages under one highly symbolic Caput rubric.
“Everybody Step”: Irving Berlin, Jazz, and Broadway in the 1920s
Authors: MAGEE JEFFREY
Published: December 2006

In his four Music Box Revues (1921–24), Irving Berlin introduced a series of songs that many construed as jazz. That view has not prevailed, but the jazz label becomes more intelligible through efforts to restore its original milieu, including the songs' distinctive musical and linguistic elements, their theatrical context, and the cultural commentary surrounding Berlin and his work in that period. At a time when the term jazz had only recently entered public discourse, and when its meaning, content, and value remained in flux, Berlin deployed a variety of ragtime and blues figures that may be described as black topics, and combined them in such a way as to produce a jazz trope, a musical construct created by juxtaposing disparate or even contradictory topics. When repeatedly set to lyrics that celebrate illicit behavior, the music gains further associations with things that jazz was thought to abet. Theatrical setting further reinforced the songs' links to jazz. Berlin wrote many of the numbers for a flapper-style sister act, often placed them in a climactic program position, and juxtaposed them with sentimental and nostalgic songs that lacked jazz flavor and whose lyrics, in some cases, pointedly denied jazz's attractions. Beyond the stage, the songs and their theatrical presentation flourished within an emerging perspective that identified Jewish Americans, such as Berlin and George Gershwin, as the key figures in jazz and musical theater. Berlin's Broadway jazz stands as an influential and revealing intersection of musical, linguistic, theatrical, and social elements in the early 1920s.
Approximate Genealogies Under Genetic Hitchhiking
Authors: Pfaffelhuber P , Haubold B , Wakolbinger A
Published: December 2006

The rapid fixation of an advantageous allele leads to a reduction in linked neutral variation around the target of selection. The genealogy at a neutral locus in such a selective sweep can be simulated by first generating a random path of the advantageous allele's frequency and then a structured coalescent in this background. Usually the frequency path is approximated by a logistic growth curve. We discuss an alternative method that approximates the genealogy by a random binary splitting tree, a so-called Yule tree that does not require first constructing a frequency path. Compared to the coalescent in a logistic background, this method gives a slightly better approximation for identity by descent during the selective phase and a much better approximation for the number of lineages that stem from the founder of the selective sweep. In applications such as the approximation of the distribution of Tajima's D, the two approximation methods perform equally well. For relevant parameter ranges, the Yule approximation is faster.
Use of Otolith Chemistry and Radiotelemetry to Determine Age‐Specific Migratory Patterns of Anadromous Bull Trout in the Hoh River, Washington
Authors: Brenkman Samuel J. , Corbett Stephen C. , Volk Eric C.
Published: December 2006

The complementary use of otolith chemistry and radiotelemetry demonstrates that bull trout Salvelinus confluentus from the Hoh River, Washington, exhibit considerable life history variability. Adult bull trout lived exclusively in the river, inhabited freshwater for prolonged periods and later became anadromous, or were anadromous and made multiple migrations between freshwater and salt water. Twenty of 40 radio‐tagged juvenile bull trout emigrated to the ocean at lengths ranging from 243 to 360 mm (mean, 287 mm), which is the first published verification of anadromy at this life history stage. Otolith chemistry analyses of 105 bull trout that were incidentally killed in commercial gill‐net fisheries revealed that 85% had migrated from freshwater to the sea at least once and that 75% had migrated multiple times. Anadromous females produced 95% of all individuals examined, but both anadromous and nonanadromous females produced progeny that were anadromous. Age at first seaward migration ranged from 3 to 6 years, 88% first emigrating to sea in their third or fourth growth year. For ages 3 and 4, anadromous individuals were larger than those that remained in freshwater. A wide size range (287–760 mm, 0.2–4.9 kg) of bull trout were killed in commercial fisheries; ages 3–5 composed 88% of the total bycatch. Relocation data from radio‐tagged juvenile and adult bull trout provided important insights on anadromous movements that helped to validate inferences drawn from widely oscillating strontium levels in otolith chemistry. In view of the direct mortality in gill‐net fisheries, an understanding of the age‐specific movements and life history variability of anadromous bull trout will be crucial to future conservation efforts, which should focus on improved monitoring of recreational and commercial bycatch in Pacific salmon fisheries.
Atrazine is an immune disruptor in adult northern leopard frogs (Rana pipiens)
Authors: Brodkin Marc A. , Madhoun Hareth , Rameswaran Muthuramanan , Vatnick Itzick
Published: December 2006

Atrazine, the most widely used herbicide in the United States, has been shown in several studies to be an endocrine disruptor in adult frogs. Results from this study indicate that atrazine also functions as an immune disruptor in frogs. Exposure to atrazine (21 ppb for 8 d) affects the innate immune response of adult Rana pipiens in similar ways to acid exposure (pH 5.5), as we have previously shown. Atrazine exposure suppressed the thioglycollate-stimulated recruitment of white blood cells to the peritoneal cavity to background (Ringer exposed) levels and also decreased the phagocytic activity of these cells. Unlike acid exposure, atrazine exposure did not cause mortality. Our results, from a dose–response study, indicate that atrazine acts as an immune disruptor at the same effective doses that it disrupts the endocrine system.
Characterizing sediment acid volatile sulfide concentrations in European streams
Authors: Burton G. Allen , Green Andrew , Baudo Renato , Forbes Valery , Nguyen Lien T. H. , Janssen Colin R. , Kukkonen Jussi , Leppanen Matti , Maltby Lorraine , Soares Amadeu , Kapo Katherine , Smith Preston , Dunning John
Published: December 2006

Sediment acid volatile sulfide (AVS) concentrations were measured in wadeable streams of a wide variety of ecoregions of western Europe (84 sites in 10 countries and nine ecoregions) to better understand spatial distribution and ecoregion relationships. Acid volatile sulfide has been shown to be a major factor controlling the bioavailability and toxicity of many common trace metals, such as Cd, Cu, Ni, Pb, and Zn. Sediment characteristics varied widely. The ratio of the sum of the simultaneously extracted metals (SEM) to AVS ranged from 0.03 to 486.59. The ΣSEM-AVS ranged from −40.02 to 17.71 μmol/g. On a regional scale, sediment characteristics such as dominant parent soil material showed significant trends in AVS distribution and variation by ecoregion. Total Fe and Mn were correlated weakly with SEM concentrations. Three AVS model approaches (i.e., the SEMAVS ratio, SEM-AVS difference, and carbon normalization) were compared at threshold exceedance levels of SEM/AVS > 9, SEM-AVS > 2, and SEM-AVS/foc > 150 μmol/g organic carbon (OC). Only 4.76% of the sediments exceeded all three AVS thresholds; 22.6% of the sediments exceeded two models; and 13% of the sediments exceeded one model only. Using the SEM:AVS, SEM-AVS, and fraction of organic carbon models, and including site-specific data and regional soil characteristics, ecoregions 1 (Portugal), 3 (Italy), 4 (Switzerland), and 9 (Belgium/Germany) had the highest potential metals toxicity; ecoregions 13 and 8 (Belgium/France) showed the lowest potential toxicity. However, because AVS can vary widely spatially and temporally, these data should not be considered as representative of the sampled ecoregions. The general relationship between AVS levels and sediment characteristics provides some predictive capability for wadeable streams in the European ecoregions.
Hepatic responses of gene expression in juvenile brown trout (Salmo trutta lacustris) exposed to three model contaminants applied singly and in combination
Authors: Krasnov Aleksei , Afanasyev Sergey , Oikari Aimo
Published: December 2006

Chemical pollution of the aquatic environment is almost always the result of multiple rather than single toxic compounds. The possibility of separating the effects of key risk chemicals from those of others, including their joint effects, is of clear theoretical interest and high technical importance. We addressed this goal using multiple gene expression profiling in the liver of juvenile brown trout (Salmo trutta lacustris) exposed to three model chemicals (cadmium, carbon tetrachloride [CCl4], and pyrene) administered singly, in binary and trinary combinations at low acutely sublethal concentrations, and in the partial dose–response manner. Differentially expressed genes were grouped by correlation of profiles, and the dependence on dose was analyzed with multiple regression. Responses to cadmium and CCl4 were largely similar, and no sign of interaction was observed (i.e., in binary combinations, the effects were equal to those produced by the more potent compound, cadmium). Joint effects became apparent in the presence of pyrene, which caused markedly different alterations in gene expression. Using the results of 118 experiments conducted earlier for comparison, we found a group of 23 genes responding to chemical toxicity (cadmium, CCl4, pyrene, and resin acids) with significantly higher probability than that of responding to other stressors (handling or viral and bacterial infections). This group included genes implicated in the immune and stress responses that were markedly enriched in extracellular proteins. In conclusion, we demonstrated that chemical-characteristic genomic endpoints often remain when the chemical is present as part of a binary or a trinary mixture. Despite dissimilar chemistry and different cellular targets, the degree of responses to the combination of cadmium and CCl4 appeared to be less than additive. Chemical interactions or nonadditive effects manifested when a compound with a markedly different mode of action (pyrene) was included into the mixture.
Effects of the estrogen agonist 17β-estradiol and antagonist tamoxifen in a partial life-cycle assay with zebrafish (Danio rerio)
Authors: van der Ven Leo T. M. , van den Brandhof Evert-Jan , Vos José H. , Wester Piet W
Published: December 2006

A partial life-cycle assay (PLC) with zebrafish (Danio rerio) was conducted to identify endocrine-disrupting effects of 17β-estradiol (E2) and tamoxifen (TMX) as reference for estrogen agonist and antagonist activity. Adult zebrafish were exposed for 21 d and offspring for another 42 d, allowing differentiation of gonads in control animals. The assessed end points included reproductive variables (egg production, fertilization, and hatching), gonad differentiation of juveniles, histopathology, and vitellogenin (VTG) expression. With E2, the most sensitive end points were feminization of offspring (at 0.1 nM) and increased VTG production in males (at 0.32 nM). At 1 nM, decreased F1 survival, increased F1 body length and weight, VTG-related edema and kidney lesions, and inhibited spermatogenesis were observed. Oocyte atresia occurred at even higher concentrations. Exposure to TMX resulted in specific effects at an intermediate test concentration (87 nM), including oocyte atresia with granulosa cell transformation and disturbed spermatogenesis (asynchrony within cysts). In F1, decreased hatching, survival, and body weight and length as well as decreased feminization were observed. Decreased vitellogenesis and egg production in females and clustering of Leydig cells in males occurred at higher concentrations. Toxicological profiles of estrogen agonists and antagonists are complex and specific; a valid and refined characterization of endocrine activity of field samples therefore can be obtained only by using a varied set of end points, including histology, as applied in the presented PLC. Evaluation of only a single end point can easily produce under- or overestimation of the actual hazard.
Efficient 3D Implementation of Local-Global Upscaling for Reservoir Simulation
Authors: Wen Xian-Huan , Durlofsky Louis J. , Chen Yuguang
Published: December 2006

Upscaling is often applied to coarsen detailed geological reservoir descriptions to sizes that can be accommodated by flow simulators. Adaptive local-global upscaling is a new and accurate methodology that incorporates global coarse-scale flow information into the boundary conditions used to compute upscaled quantities (e.g., coarse-scale transmissibilities). The procedure is iterated until a self-consistent solution is obtained. In this work, we extend this approach to 3D systems and introduce and evaluate procedures to decrease the computational demands of the method. This includes the use of purely local upscaling calculations for the initial estimation of coarse-scale transmissibilities and the use of reduced border regions during the iterations. This is shown to decrease the computational requirements of the reduced procedure significantly relative to the full methodology, while impacting the accuracy very little. The performance of the adaptive local-global upscaling technique is evaluated for three different heterogeneous reservoir descriptions. The method is shown to provide a high degree of accuracy for relevant flow quantities. In addition, it is shown to be less computationally demanding and significantly more accurate than some existing extended local upscaling procedures.

Introduction

Fine-scale heterogeneity can have a significant impact on reservoir performance. Because it is usually not feasible to simulate directly on the detailed geocellular model, some type of upscaling is often applied to generate the simulation model from the geological description. Here, we focus on the upscaling of single-phase flow parameters, particularly absolute permeability. The algorithms we consider can provide either coarse-scale permeability, designated k*, or coarse-scale transmissibility, designated T* . It is important to emphasize that the accurate upscaling of permeability (which can be studied within the context of single-phase flow) is essential for the development of accurate coarse models of two-phase or multiphase flow. Thus the applicability of the methods developed here is very broad and includes all types of displacement processes.
Quantifying Uncertainty for the PUNQ-S3 Problem in a Bayesian Setting With RML and EnKF
Authors: Gao Guohua , Zafari Mohammad , Reynolds Albert C.
Published: December 2006

The well known PUNQ-S3 reservoir model represents a synthetic problem which was formulated to test the ability of various methods and research groups to quantify the uncertainty in the prediction of cumulative oil production. Previous results reported on this project suggest that the randomized maximum likelihood (RML) method gives a biased characterization of the uncertainty. A major objective of this paper is to show that this is incorrect. With a correct implementation of the RML method within a Bayesian framework, we show that RML does an adequate job of sampling the a posteriori distribution for the PUNQ problem. In particular, the true predicted oil production lies within the band of predictions generated with the RML method and is not biased. We also apply the ensemble Kalman filter (EnKF) method to the PUNQ data set, and show that this method also gives a reasonable quantification of the uncertainty in performance predictions with an uncertainty range similar to the one obtained with RML.
Diversity, habitat use and conservation of freshwater molluscs in the lower Guadiana River basin (SW Iberian Peninsula)
Authors: Pérez‐Quintero Juan Carlos
Published: December 2006

A study on the distribution pattern and conservation of freshwater molluscs of the south Guadiana River (SW Iberian Peninsula) was carried out between the Alqueva dam and the Atlantic Ocean.

The knowledge of the distribution and abundance of molluscs before the closure of the Alqueva dam is an important tool for evaluating the potential reduction in diversity and the changes in species conservation status that may occur later.

Twenty‐three species (15 gastropods and 8 bivalves) were found in the study area. The presence of Unio crassus and Potomida littoralis indicates the importance of this basin for the conservation of endangered mussels (Unionidae) in the south Iberian Peninsula.

Drainage area above the sampling site explained almost 58% of the variation in species richness. Larger drainage areas had a higher number of species, including those endemic to the basin.

Patterns of habitat use were examined to identify species preferences with respect to the erosional‐depositional gradient. Islamia minuta, Pisidium casertanum and Pisidium personatum find their optimum habitat in headwaters, whereas Theodoxus fluviatilis, Mercuria emiliana, Radix auricularia and all unionid species inhabit large and stable habitats downstream without marine influence.

Populations of invasive Corbicula fluminea were found in the Guadiana River basin, both in rivers with large drainage areas and in brackish waters near the mouths of rivers.

Copyright © 2006 John Wiley & Sons, Ltd.
A case study on the population ecology of a topmouth gudgeon (Pseudorasbora parva) population in the UK and the implications for native fish communities
Authors: Britton J.R. , Davies G.D. , Brazier M. , Pinder A.C.
Published: December 2006

The topmouth gudgeon Pseudorasbora parva is a small Asian cyprinid species that has proved invasive throughout many European countries. Following an initial introduction into the wild in 1996, the species is now proving invasive in the UK, with at least 25 infested waters in England and Wales, of which 10 are known to have direct connection to a major river catchment.

To demonstrate the threat of P. parva to fisheries in the UK, a case study is presented on a lake located in the Lake District of England where the species was introduced in 2000. The species rapidly established a breeding population that, by 2003, was the dominant species in size classes <70 mm. In 2004, they were the only species in the lake that produced young‐of‐the‐year.

Individual P. parva adopted the reproductive tactics of early maturity, multiple spawning, male dominance and male nest guarding; sexual dimorphism was manifested in larger body size of males. These traits were in contrast to the resident, native species of the lake, including roach Rutilus rutilus and gudgeon Gobio gobio, which adopted traits of later maturity and single spawning.

This case study, therefore, revealed relatively rapid establishment of a P. parva population, their subsequent numerical dominance of the fish community, and the impediment of the recruitment of native fish. The implications for UK fisheries are concerning: should P. parva continue to disperse and individuals adopt similar traits as those in this case study, there may be few waters immune from their invasion, numerical dominance and subsequent impacts.

Copyright © 2006 John Wiley & Sons, Ltd.
Redips: Backlink search and analysis on the Web for business intelligence analysis
Authors: Chau Michael , Shiu Boby , Chan Ivy , Chen Hsinchun
Published: December 2006

The World Wide Web presents significant opportunities for business intelligence analysis as it can provide information about a company's external environment and its stakeholders. Traditional business intelligence analysis on the Web has focused on simple keyword searching. Recently, it has been suggested that the incoming links, or backlinks, of a company's Web site (i.e., other Web pages that have a hyperlink pointing to the company of interest) can provide important insights about the company's “online communities.” Although analysis of these communities can provide useful signals for a company and information about its stakeholder groups, the manual analysis process can be very time‐consuming for business analysts and consultants. In this article, we present a tool called Redips that automatically integrates backlink meta‐searching and text‐mining techniques to facilitate users in performing such business intelligence analysis on the Web. The architectural design and implementation of the tool are presented in the article. To evaluate the effectiveness, efficiency, and user satisfaction of Redips, an experiment was conducted to compare the tool with two popular business intelligence analysis methods—using backlink search engines and manual browsing. The experiment results showed that Redips was statistically more effective than both benchmark methods (in terms of Recall and F‐measure) but required more time in search tasks. In terms of user satisfaction, Redips scored statistically higher than backlink search engines in all five measures used, and also statistically higher than manual browsing in three measures.
Digital information support for domestic violence victims
Authors: Westbrook Lynn
Published: December 2006

With domestic violence directly impacting over 5 million victims in the United States annually, the growing e‐health and e‐government networks are developing digitally based resources for both victims and those who aid them. The well‐established community information and referral role of public libraries dovetails with this digital referral network model; however, no study of the actual service provided by public libraries is available. This examination of e‐mail reference responses to requests for safe‐house contact information revealed major gaps in cyber‐safety awareness and uneven implementation of professional standards for virtual reference service. Implications for information system design, professional standards, education, and future research are discussed.
Statistical modelling for process control in the sawmill industry
Authors: Beran Rudolf
Published: December 2006

Softwood logs are processed into green boards through a series of horizontal or vertical sawing operations that reduce lumber thickness. This paper uses physical understanding to model how systematic and random errors in board thickness accumulate during sequential resawing. The error model is validated on board thickness measurements gathered at a northern California sawmill. The analysis

explains previously puzzling patterns in the spatially averaged sample variances of board thickness measurements;

enables estimating, from measured board thicknesses, the means and variances of the thickness errors introduced by each sawing operation in the observed sequence;

generates stronger methods for sawmill quality control.

Through submodelling of the mean vector and the covariance matrix of measured thicknesses, the paper finds slight ‘wedging’ in the mean thickness of certain boards and distance‐based correlations among the random sawing errors on these boards. The one‐way random effects model, used uncritically in earlier analyses of lumber thickness measurements, does not fit the study data. Copyright © 2006 John Wiley & Sons, Ltd.
Mixture distribution‐based forecasting using stochastic volatility models
Authors: Clements A. E. , Hurn S. , White S. I.
Published: December 2006

Many traditional econometric methods forecast the conditional distribution of asset returns by a point prediction of volatility. Alternatively, forecasts of this distribution may be generated from a mixture of distributions. This paper proposes a method by which information extracted from the estimation of a standard stochastic volatility model (using non‐linear filtering) can be used to generate mixture distribution forecasts. In general, it is found that forecasts based on mixture distributions are superior to those simply using point predictions of volatility. In terms of mixture distribution forecasts, the method proposed in this paper is found to be superior to a number of competing approaches. Copyright © 2006 John Wiley & Sons, Ltd.
Bayesian predictive inference under informative sampling and transformation
Authors: Nandram Balgobin , Won Choi Jai , Shen Gang , Burgos Corinne
Published: December 2006

We consider the problem in which a biased sample is selected from a finite population (a random sample from a super‐population), and inference is required for the finite population mean and the super‐population mean. The selection probabilities are linearly related to the measurements, providing a non‐ignorable selection model. When all the selection probabilities are known, as in our problem, inference about the finite population mean and the super‐population mean can be made. As a practical issue, our method requires normality, but the measurements are not necessarily normally distributed. Thus, the key issue is the dilemma that a transformation to normality is needed, but this transformation will destroy the linearity between the selection probabilities and the measurements. This is the key issue we address in this work. We use the Gibbs sampler and the sample importance resampling algorithm to fit the non‐ignorable selection model to a simple example on natural gas production. Our non‐ignorable selection model estimates the finite population mean production much closer to the true finite population mean than a model which ignores the selection probabilities, and there is improved precision of the non‐ignorable selection model over this latter model. A naive 95% credible interval based on the Horvitz–Thompson estimator is too wide. Copyright © 2006 John Wiley & Sons, Ltd.
Colour harmonization in car manufacturing processes
Authors: Andriyashin A. , Benko M. , Härdle W. , Timofeev R. , Ziegenhagen U.
Published: December 2006

One of the major cost factors in car manufacturing is the painting of the body and other parts such as the wing or bonnet. Surprisingly, the painting may be even more expensive than the body itself. From this point of view it is clear that car manufacturers need to observe the painting process carefully to avoid any deviations from the desired result. Especially for metallic colours where the shining is based on microscopic aluminium particles, customers tend to be very sensitive towards a difference in the light reflection of different parts of the car.

The following study, carried out in close co‐operation with a partner from car industry, combines classical tests and non‐parametric smoothing techniques to detect trends in the process of car painting. The localized versions motivated by t‐test, Mann–Kendall, Cox–Stuart and a change point test are employed in this study. Suitable parameter settings and the properties of the proposed tests are studied by simulations based on resampling methods borrowed from non‐parametric smoothing.

The aim of the analysis is to find a reliable technical solution which avoids any interaction from the human side. Copyright © 2006 John Wiley & Sons, Ltd.
Damping factor in Google page ranking
Authors: Fu Hwai‐Hui , Lin Dennis K. J. , Tsai Hsien‐Tang
Published: December 2006

Google, the largest search engine worldwide, adopts PageRank technology to determine the rank of website listings. This paper describes how damping factor is a critical factor in changing a website's ranking in traditional Google PageRank technology. A modified algorithm based on input–output ratio concept is proposed to substitute for the damping factor. Besides there is no need to choose an optimal damping factor value, the modified algorithm has an equivalent effect on computation as the traditional Google's PageRank algorithm. Copyright © 2006 John Wiley & Sons, Ltd.
Multiple Targeted Therapies: Is there a Place for Vach Type‐3 or Type‐4 Design Trials
Authors: Hasenclever Dirk
Published: December 2006

Invited comment on Vach W. and dePoint Christensen R. (2006). Making efficient use of patients in designing phase III trials investigating simultaneously a set of targeted therapies with different targets, Biometrical Journal 48, 897–907.

For complexity reasons the designs proposed by Vach et al. will probably not be used in initial drug registration trials. But they may be an option for established study groups that run treatment‐optimisation or indication‐extension trials investigating targeted drugs that are already registered. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Decolourisation of a synthetic textile effluent using a bacterial consortium
Authors: Ramalho Patrícia A. C. F. , Cardoso M. Helena , Ramalho M. Teresa , Gübitz Georg M. , Cavaco‐Paulo Artur M.
Published: December 2006

In the present study we examined the performance of a thermoalkalophilic bacterial consortium, where the predominant strain was Bacillus sp. SF, in the degradation of Reactive Black 5 (RB5). We used a reactor working in continuous mode and investigated the effects of pH, hydraulic retention time (HRT) and several added salts on colour and chemical oxygen demand (COD) reductions. For the chosen operational conditions (pH 9, 55°C and HRT of 12 h) the efficiencies achieved were 91.2 ± 0.8 % for colour removal and 81.2% for COD removal. The system tolerated, with no significant decrease in colour removal efficiency, 30 g/L Na2SO4, Na2CO3 or NaCl. The latter two salts, however, led to a reduction in COD removal of 30% and 50%, respectively. The system proved to be very effective in the decolourisation of C.I. RB5 under alkaline conditions and at a comparatively high temperature.
Recent progress in engineering α/β hydrolase‐fold family members
Authors: Qian Zhen , Fields Christina J. , Yu Ying , Lutz Stefan
Published: December 2006

The members of the α/β hydrolase‐fold family represent a functionally versatile group of enzymes with many important applications in biocatalysis. Given the technical significance of α/β hydrolases in processes ranging from the kinetic resolution of enantiomeric precursors for pharmaceutical compounds to bulk products such as laundry detergent, optimizing and tailoring enzymes for these applications presents an ongoing challenge to chemists, biochemists, and engineers alike. A review of the recent literature on α/β hydrolase engineering suggests that the early successes of “random processes” such as directed evolution are now being slowly replaced by more hypothesis‐driven, focused library approaches. These developments reflect a better understanding of the enzymes' structure‐function relationship and improved computational resources, which allow for more sophisticated search and prediction algorithms, as well as, in a very practical sense, the realization that bigger is not always better.
Insight into the mechanism of fast movement of myosin from Chara corallina
Authors: Sumiyoshi Hiroki , Ooguchi Masami , Ooi Atsushi , Okagaki Tsuyoshi , Higashi‐Fujime Sugie
Published: December 2006

Chara myosin, two‐headed plant myosin belonging to class XI, slides F‐actin at maximally 60 μm s−1. To elucidate the mechanism of this fast sliding, we extensively investigated its mechanochemical properties. The maximum actin activated ATPase activity, Vmax, was 21.3 s−1 head−1 in a solution, but when myosin was immobilized on the surface, its activity was 57.6 s−1 head−1 at 2 mg ml−1 of F‐actin. The sliding velocity and the actin activated ATPase activity were greatly inhibited by ADP, suggesting that ADP dissociation was the rate limiting step. With the extensive assay of motility by varying the surface density, the duty ratio of Chara myosin was found to be 0.49–0.44 from velocity measurements and 0.34 from the landing rate analysis. At the surface density of 10 molecules μm−2, Chara myosin exhibited pivot movement under physiological conditions. Based on the results obtained, we will discuss the sliding mechanism of Chara myosin according to the working stroke model in terms of its physiological aspects. aspects. Cell Motil. Cytoskeleton 2007. © 2006 Wiley‐Liss, Inc.
MEK/ERK regulates adherens junctions and migration through Rac1
Authors: Ray Ramesh M. , Vaidya Rajiv J. , Johnson Leonard R.
Published: December 2006

Polyamine depletion with the ornithine decarboxylase inhibitor α‐difluoromethyl ornithine (DFMO), prevents Rac1 activation causing the formation of a thick actin cortex at the cell periphery and inhibits migration of intestinal epithelial cells. In the present study, we demonstrate that MEK activation by EGF increased Rac1 activation, dissociation of intercellular contacts, and migration in both control and polyamine‐depleted cells, while U0126, a specific inhibitor of MEK1, prevented disruption of junctions as well as EGF‐induced Rac1 activation. Constitutively active MEK1 (CA‐MEK) expression altered cell–cell contacts in control and polyamine depleted cells. The expression of constitutively active Rac1 (CA‐Rac1) restored β‐catenin to the cell periphery and prevented the formation of actin cortex and caused the appearance of F‐actin stress fibers in polyamine‐depleted cells. Inhibition of Rac activation by NSC23766, a specific inhibitor of Tiam1, an upstream guanidine nucleotide exchange factor for Rac1, reproduced the β‐catenin localization and actin structure of polyamine‐depleted cells. Tiam1 localized more extensively with β‐catenin at the cell periphery in CA‐Rac1 cells compared to vector cells. Polyamine depletion decreased the expression of E‐cadherin to a greater extent compared to β‐catenin. Subcellular fractionation further confirmed our immuno‐localization and western blotting observations. These data suggest that EGF acting through MEK1/ERK to activate Rac1 regulates cell–cell contacts. Thus, decreased migration in polyamine depleted cells may be due to the inhibition of Tiam1 activation of Rac1 and the subsequent decreased expression of β‐catenin and E‐cadherin leading to reduced cell–cell contacts. Cell Motil. Cytoskeleton 2007. © 2006 Wiley‐Liss, Inc.