bluuebunny/crossref_metadata_2025_split huggingface dataset:
A geochemical framework for the application of stable sulphur isotopes to fossil pyritization
Authors: RAISWELL R. 
Published: December 2007

Pyrite formation is associated with fossils where the organic material decays by sulphate reduction, or where the carbonate skeleton acts either as a nucleation substrate or induces iron sulphide precipitation by dissolution. These requirements define specific combinations of porewater chemistry and saturation state with respect to carbonates and iron sulphides. A review of modern marine sediments suggests that near-surface porewaters are always over-saturated, or close to saturation, with iron sulphides but are alternately rich in either dissolved iron or dissolved sulphide. However, significant variations in carbonate saturation state may occur, with porewaters being undersaturated in the early stages of sulphate reduction, but subsequently becoming oversaturated until the later stages of methanogenesis. Here undersaturation may return if there is a substantial input of carbon dioxide, and if little alkalinity has arisen from iron reduction.
Organic matter pyritization requires that soft-tissue material decays by sulphate reduction to release dissolved sulphide, with dissolved iron supplied by the surrounding porewaters. The modern sediment studies therefore suggest that organic matter pyritization can occur only during the earliest stages of sulphate reduction, where there are iron-rich porewaters which are saturated with iron sulphides. Pyrite replacement of carbonate shell material requires porewater undersaturation with respect to carbonates and analogy with modern sediments suggests that these conditions occur either during the earliest stages of sulphate reduction, or when methanogenesis produces undersaturation. Between these periods porewaters are saturated with respect to carbonates and pyrite of different morphologies can precipitate on carbonate shells. Sulphur isotope data provide support for these associations of porewater chemistry and style of fossil pyritization. The best-described examples are for soft tissue pyritization in Beecher's Trilobite Bed (Ordovician) and the Hünsruck Slate (Devonian), where the isotopic data are consistent with rapid, early pyritization in iron-rich porewaters. More data are needed on shell pyritization with the range of isotopic compositions indicating formation through all stages of diagenesis.
Tectonic, magmatic and depositional processes at passive continental margins
Authors: ROBERTS ALAN M. , KUSZNIR NICK J. 
Published: December 2007

The papers presented in this thematic collection all derive from a meeting on geological processes at passive margins, held at Burlington House in February 1996. The meeting was co-hosted by the Geological Society, The Norwegian Geological Society and The Norwegian Petroleum Society. We would like to thank our colleagues Bjørn Larsen and Olav Eldholmfor ensuring the strong Norwegian participation at the meeting and Mike Daly for organizing contributions from the UK hydrocarbon industry.

The formation of passive continental margins during continental rifting to form new oceans is a fundamental component of the plate tectonic process yet many aspects of the formation of passive margins are still poorly understood. Passive margins are amongst the more difficult areas of the earth's surface to study, because of their great water depths and the difficulty of acquiring data. Much of the current upsurge of attention to passive continental margins, which is particularly strong for the Irish, UK and Norwegian Atlantic margins, arises from the increased interest in their hydrocarbon potential resulting from advances in deep water exploration and production technology. This renewed interest has led to the collection of new data and the increased exchange of ideas between industry and academia, some of the results of which are presented here.
The successful geological analysis of passive margins calls for the integration of many different disciplines. The papers presented here show how we need to understand the link between tectonics, depositional systems and magmatic processes in order to understand margin evolution. In addition much of
Mesozoic-Cenozoic evolution of the intraplate Euphrates fault system, Syria: implications for regional tectonics
Authors: LITAK ROBERT K. , BARAZANGI MUAWIA , BEAUCHAMP WELDON , SEBER DOGAN , BREW GRAHAM , SAWAF TARIF , AL-YOUSSEF WASIF 
Published: December 2007

A lack of dramatic surface geological structures along the Euphrates River in Syria belie a complex tectonic history revealed by newly released seismic reflection and well data. We document the intraplate Euphrates fault system, characterize the variation in structural style along its 350 km length in Syria, and infer its Mesozoic-Cenozoic tectonic and deformational history. We then relate the deformation of the Euphrates system and other proximate intraplate structures to nearby Arabian plate boundary processes in order to develop a new model for the tectonic evolution of the northern Arabian plate.
Throughout most of Mesozoic time, the Euphrates area experienced minor deposition compared to the Palmyride trough to its southwest, and the Sinjar trough to its northeast. During latest Cretaceous time, however, significant sinistral transtension occurred along the length of the Euphrates fault system in Syria, with graben formation especially noteworthy in southeastern Syria. This episode was probably related to events at nearby plate boundaries, and may have reactivated a zone of weakness formed during Pan-African accretion of the Arabian plate. A Palaeogene sag basin formed over the graben system in southeastern Syria. Neogene continental collision along the northern and eastern Arabian plate boundaries caused minor reactivation of the Euphrates fault system in a dextral transpressional sense, in concert with significant inversion and the main phase of uplift of the nearby Palmyride and Sinjar mountains.
Multiphase reddening and weathering events in Upper Carboniferous red beds from the English West Midlands
Authors: JOHNSON S. A. , GLOVER B. W. , TURNER P. 
Published: December 2007

Sediments of the Halesowen and Salop Formations (Westphalian D-Stephanian) in the West Midlands were deposited on the southern margin of the Pennine Basin during a period of relative tectonic quiescence during the Variscan Orogeny. The clastic framework of the predominantly red sandstones and mudstones in the Salop Formation includes large detrital hematite grains; these yield a primary component of magnetization indicating that sediments were deposited close to the Carboniferous palaeo-equator. Variscan uplift, erosion and subsequent deep oxidation in an arid climate during the Permian resulted in the precipitation of finer hematite in rocks of both formations (which are now found at depths of over 150 m below the present-day ground level). These grains carry secondary magnetizations which indicate formation at palaeolatitudes of between 5° and 15°N, the position that Britain occupied during the Permian.
The pattern of Permian remagnetization (particularly in borehole samples) suggests that the secondary fine-grained hematite was precipitated as a result of lateral flow of meteoric water through connected, permeable sandstone units, rather than downward percolation through the entire succession. Present-day surface weathering has resulted in the dissolution of the finer grains of hematite and, in some cases, where permeabilities are relatively high, it has also affected the coarser fraction. Consequently, the record of late Carboniferous and Permian magnetization events is commonly incomplete in strata close to the present day ground level.
Mantle plumes and Antarctica-New Zealand rifting: evidence from mid-Cretaceous mafic dykes
Authors: STOREY BRYAN C. , LEAT PHILIP T. , WEAVER STEPHEN D. , PANKHURST ROBERT J. , BRADSHAW JOHN D. , KELLEY SIMON 
Published: December 2007

Ocean floor magnetic anomalies show that New Zealand was the last continental fragment to separate from Antarctica during Gondwana break-up, drifting from Marie Byrd Land, West Antarctica, about 84 Ma ago. Prior to continental drift, a voluminous suite of mafic dykes (dated by Ar–Ar laser stepped heating at 107 ± 5 Ma) and anorogenic silicic rocks, including syenites and peralkaline granitoids (95–102 Ma), were emplaced in Marie Byrd Land during a rifting event. The mafic dyke suite includes both high- and low-Ti basalts. Trace element and Sr and Nd isotope compositions of the mafic dykes may be modelled by mixing between tholeiitic OIB (asthenosphere-derived) and alkaline high- to low-Ti alkaline magmas (lithospheric mantle derived). Pb isotopes indicate that the OIB component had a HIMU composition.
We suggest that the rift-related magmatism was generated in the vicinity of a mantle plume. The plume helped to control the position of continental separation within the very wide region of continental extension that developed when the Pacific–Phoenix spreading ridge approached the subduction zone. Separation of New Zealand from Antarctica occurred when the Pacific–Phoenix spreading centre propagated into the Antarctic continent. Sea floor spreading in the region of the mantle plume may have caused an outburst of volcanism along the spreading ridge generating an oceanic plateau, now represented by the 10–15 km thick Hikurangi Plateau situated alongside the Chatham Rise, New Zealand. The plateau consists of tholeiitic OIB-MORB basalt, regarded as Cretaceous in age, and similar in composition to the putative tholeiitic end-member in the Marie Byrd Land dykes. The mantle plume is proposed to now underlie the western Ross Sea, centred beneath Mount Erebus, where it was largely responsible for the very voluminous, intraplate, alkaline McMurdo Volcanic Group. A second mantle plume beneath Marie Byrd Land formed the Cenozoic alkaline volcanic province.
Effects of CMP Slurry Chemistry on Agglomeration of Alumina and Copper Surface Hardness
Authors: Ihnfeldt Robin V. , Talbot Jan B. 
Published: December 2007

The influence of common slurry additives on the colloidal	behavior of alumina suspensions and the surface characteristics of copper were investigated. The effects of	the addition of glycine and H2O2 to aqueous suspensions of alpha-alumina at various pH values were studied by zeta	potential and agglomerate size distribution measurements. Depending on the state of copper in solution, alumina agglomerate size was found to either increase or decrease. Nanohardness of 1 µm copper films deposited onto 30 nm Ta on a silicon wafer was measured after exposure to the same slurry solutions and was found to be significantly affected by pH and addition of chemical additives. The agglomeration behavior	and hardness measurements suggest that the states of the copper in solution or on the surface are consistent with potential-pH diagrams.
Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering
Authors: Jagalur Manjunatha , Pal Chris , Learned-Miller Erik , Zoeller R Thomas , Kulp David 
Published: December 2007

AbstractBackgroundMany important high throughput projects usein situhybridization and may require the analysis of images of spatial cross sections of organisms taken with cellular level resolution. Projects creating gene expression atlases at unprecedented scales for the embryonic fruit fly as well as the embryonic and adult mouse already involve the analysis of hundreds of thousands of high resolution experimental images mapping mRNA expression patterns. Challenges include accurate registration of highly deformed tissues, associating cells with known anatomical regions, and identifying groups of genes whose expression is coordinately regulated with respect to both concentration and spatial location. Solutions to these and other challenges will lead to a richer understanding of the complex system aspects of gene regulation in heterogeneous tissue.ResultsWe present an end-to-end approach for processing rawin situexpression imagery and performing subsequent analysis. We use a non-linear, information theoretic based image registration technique specifically adapted for mapping expression images to anatomical annotations and a method for extracting expression information within an anatomical region. Our method consists of coarse registration, fine registration, and expression feature extraction steps. From this we obtain a matrix for expression characteristics with rows corresponding to genes and columns corresponding to anatomical sub-structures. We perform matrix block cluster analysis using a novel row-column mixture model and we relate clustered patterns to Gene Ontology (GO) annotations.ConclusionResulting registrations suggest that our method is robust over intensity levels and shape variations in ISH imagery. Functional enrichment studies from both simple analysis and block clustering indicate that gene relationships consistent with biological knowledge of neuronal gene functions can be extracted from large ISH image databases such as the Allen Brain Atlas [1] and the Max-Planck Institute [2] using our method. While we focus here on imagery and experiments of the mouse brain our approach should be applicable to a variety ofin situexperiments.
Mitochondrial DNA heteroplasmy in ovine fetuses and sheep cloned by somatic cell nuclear transfer
Authors: Burgstaller Jörg P , Schinogl Pamela , Dinnyes Andras , Müller Mathias , Steinborn Ralf 
Published: December 2007

Abstract

Background
The mitochondrial DNA (mtDNA) of the cloned sheep "Dolly" and nine other ovine clones produced by somatic cell nuclear transfer (SCNT) was reported to consist only of recipient oocyte mtDNA without any detectable mtDNA contribution from the nucleus donor cell. In cattle, mouse and pig several or most of the clones showed transmission of nuclear donor mtDNA resulting in mitochondrial heteroplasmy. To clarify the discrepant transmission pattern of donor mtDNA in sheep clones we analysed the mtDNA composition of seven fetuses and five lambs cloned from fetal fibroblasts.

Results
The three fetal fibroblast donor cells used for SCNT harboured low mtDNA copy numbers per cell (A: 753 ± 54, B: 292 ± 33 and C: 561 ± 88). The ratio of donor to recipient oocyte mtDNAs was determined using a quantitative amplification refractory mutation system (ARMS) PCR (i.e. ARMS-qPCR). For quantification of SNP variants with frequencies below 0.1% we developed a restriction endonuclease-mediated selective quantitative PCR (REMS-qPCR). We report the first cases (n = 4 fetuses, n = 3 lambs) of recipient oocyte/nuclear donor mtDNA heteroplasmy in SCNT-derived ovine clones demonstrating that there is no species-effect hindering ovine nucleus-donor mtDNA from being transmitted to the somatic clonal offspring. Most of the heteroplasmic clones exhibited low-level heteroplasmy (0.1% to 0.9%, n = 6) indicating neutral transmission of parental mtDNAs. High-level heteroplasmy (6.8% to 46.5%) was observed in one case. This clone possessed a divergent recipient oocyte-derived mtDNA genotype with three rare amino acid changes compared to the donor including one substitution at an evolutionary conserved site.

Conclusion
Our study using state-of-the-art techniques for mtDNA quantification, like ARMS-qPCR and the novel REMS-qPCR, documents for the first time the transmission of donor mtDNA into somatic sheep clones. MtDNA heteroplasmy was detected in seven of 12 clones tested, whereby all but one case revealed less than 1% mtDNA contribution from the nuclear donor cell suggesting neutral segregation.
Comparative genomic characterization of citrus-associated Xylella fastidiosa strains
Authors: da Silva Vivian S , Shida Cláudio S , Rodrigues Fabiana B , Ribeiro Diógenes CD , de Souza Alessandra A , Coletta-Filho Helvécio D , Machado Marcos A , Nunes Luiz R , de Oliveira Regina Costa 
Published: December 2007

Abstract

Background
The xylem-inhabiting bacterium Xylella fastidiosa (Xf) is the causal agent of Pierce's disease (PD) in vineyards and citrus variegated chlorosis (CVC) in orange trees. Both of these economically-devastating diseases are caused by distinct strains of this complex group of microorganisms, which has motivated researchers to conduct extensive genomic sequencing projects with Xf strains. This sequence information, along with other molecular tools, have been used to estimate the evolutionary history of the group and provide clues to understand the capacity of Xf to infect different hosts, causing a variety of symptoms. Nonetheless, although significant amounts of information have been generated from Xf strains, a large proportion of these efforts has concentrated on the study of North American strains, limiting our understanding about the genomic composition of South American strains – which is particularly important for CVC-associated strains.

Results
This paper describes the first genome-wide comparison among South American Xf strains, involving 6 distinct citrus-associated bacteria. Comparative analyses performed through a microarray-based approach allowed identification and characterization of large mobile genetic elements that seem to be exclusive to South American strains. Moreover, a large-scale sequencing effort, based on Suppressive Subtraction Hybridization (SSH), identified 290 new ORFs, distributed in 135 Groups of Orthologous Elements, throughout the genomes of these bacteria.

Conclusion
Results from microarray-based comparisons provide further evidence concerning activity of horizontally transferred elements, reinforcing their importance as major mediators in the evolution of Xf. Moreover, the microarray-based genomic profiles showed similarity between Xf strains 9a5c and Fb7, which is unexpected, given the geographical and chronological differences associated with the isolation of these microorganisms. The newly identified ORFs, obtained by SSH, represent an approximately 10% increase in our current knowledge of the South American Xf gene pool and include new putative virulence factors, as well as novel potential markers for strain identification. Surprisingly, this list of novel elements include sequences previously believed to be unique to North American strains, pointing to the necessity of revising the list of specific markers that may be used for identification of distinct Xf strains.
Simulating non-small cell lung cancer with a multiscale agent-based model
Authors: Wang Zhihui , Zhang Le , Sagotsky Jonathan , Deisboeck Thomas S 
Published: December 2007

Abstract

Background
The epidermal growth factor receptor (EGFR) is frequently overexpressed in many cancers, including non-small cell lung cancer (NSCLC). In silico modeling is considered to be an increasingly promising tool to add useful insights into the dynamics of the EGFR signal transduction pathway. However, most of the previous modeling work focused on the molecular or the cellular level only, neglecting the crucial feedback between these scales as well as the interaction with the heterogeneous biochemical microenvironment.

Results
We developed a multiscale model for investigating expansion dynamics of NSCLC within a two-dimensional in silico microenvironment. At the molecular level, a specific EGFR-ERK intracellular signal transduction pathway was implemented. Dynamical alterations of these molecules were used to trigger phenotypic changes at the cellular level. Examining the relationship between extrinsic ligand concentrations, intrinsic molecular profiles and microscopic patterns, the results confirmed that increasing the amount of available growth factor leads to a spatially more aggressive cancer system. Moreover, for the cell closest to nutrient abundance, a phase-transition emerges where a minimal increase in extrinsic ligand abolishes the proliferative phenotype altogether.

Conclusion
Our in silico results indicate that in NSCLC, in the presence of a strong extrinsic chemotactic stimulus (and depending on the cell's location) downstream EGFR-ERK signaling may be processed more efficiently, thereby yielding a migration-dominant cell phenotype and overall, an accelerated spatio-temporal expansion rate.
C-Reactive Protein and All-Cause Mortality in a Large Hospital-Based Cohort
Authors: Marsik Claudia , Kazemi-Shirazi Lili , Schickbauer Thomas , Winkler Stefan , Joukhadar Christian , Wagner Oswald F , Endler Georg 
Published: December 2007

Abstract
Background: C-reactive protein (CRP), an acute-phase protein, is a sensitive systemic marker of inflammation and acute-phase reactions. Testing CRP concentrations at hospital admission may provide information about disease risk and overall survival.
Methods: All first-ever transmittals to the department of medical and chemical laboratory diagnostics for determination of low-sensitivity CRP (n = 274 515, 44.5% male, median age 51 years) between January 1991 and July 2003 were included [median follow-up time: 4.4 years (interquartile range, 2.3–7.4 years)]. The primary endpoint was all-cause mortality. Multivariate Cox regression adjusted for sex and age was applied for analysis.
Results: Compared to individuals within the reference category (CRP &lt;5 mg/L), hazard ratios (HR) for all-cause mortality increased from 1.4 (5–10 mg/L category) to 3.3 in the highest category (&gt;80 mg/L, all P &lt;0.001). CRP was associated with various causes of death. The relation of CRP to cancer death was stronger than to vascular death. Younger patients with increased CRP had relatively far worse outcome than older patients (maximal HR: ≤30 years: 6.7 vs &gt;60 years: 1.7–3.7). Interestingly, both short- and long-term mortality were associated with increasing CRP concentrations (&gt;80 mg/L: HR 22.8 vs 1.4).
Conclusion: Measurement of low-sensitivity CRP at hospital admission allowed for the identification of patients at increased risk of unfavorable outcome. Our findings indicate that close attention should be paid to hospitalized patients with high CRP not only because of very substantial short-term risk, but also long-term excess risk, the basis for which needs to be determined.
Michael Jaeger, Fausts Kolonie. Goethes kritische Phänomenologie der Moderne. 2004
Authors: Westerhoff Armin 
Published: December 2007

Die Illustrationen auf dem Titelblatt von Michael Jaegers Habilitationsschrift Fausts Kolonie wecken starke Erwartungen. Hier findet man zwei historische Fotos aus dem Jahre 1913, die Arbeiter und Maschinen bei den Fronarbeiten zum Bau des Panama-Kanals zeigen; durch futuristisch anmutende Verstrebungen miteinander verbunden, bilden diese beiden Bilder die eine Seite eines graphischen Zeichens, auf dessen anderer (Umschlag-)Seite vier Verse aus dem letzten Akt von Goethes Faust II in dieselben Verstrebungen eingetragen sind:
Doch sei der Lindenwuchs vernichtet
Zu halbverkohlter Stämme Graun,
Ein Luginsland ist bald errichtet,
Um ins Unendliche zu schaun. (V. 11342–11345)
Diese Gegenüberstellung von Bild und Zitat lenkt das Interesse des Lesers: Man erwartet, daß hier der Bogen gespannt werden würde von Fausts Allmachtsphantasien gegen Ende des Faust II, als dieser sich zum Herrscher über Land und Meer aufschwingen will und dabei die Idylle von Philemon und Baucis – den „Lindenwuchs“ (V. 11342) – opfert, zu der im 19. Jahrhundert tatsächlich einsetzenden Herrschaft des „Maschinenwesens“ (Goethe), für welche die Durchbohrung der Landenge zwischen Atlantik und pazifischem Ozean in Panama ein besonders auffälliges Beispiel liefert.