bluuebunny/crossref_metadata_2025_split huggingface dataset:
Function, Structure, and Evolution of the RubisCO-Like Proteins and Their RubisCO Homologs
Authors: Tabita F. Robert , Hanson Thomas E. , Li Huiying , Satagopan Sriram , Singh Jaya , Chan Sum 
Published: December 2007

SUMMARYAbout 30 years have now passed since it was discovered that microbes synthesize RubisCO molecules that differ from the typical plant paradigm. RubisCOs of forms I, II, and III catalyze CO2fixation reactions, albeit for potentially different physiological purposes, while the RubisCO-like protein (RLP) (form IV RubisCO) has evolved, thus far at least, to catalyze reactions that are important for sulfur metabolism. RubisCO is the major global CO2fixation catalyst, and RLP is a somewhat related protein, exemplified by the fact that some of the latter proteins, along with RubisCO, catalyze similar enolization reactions as a part of their respective catalytic mechanisms. RLP in some organisms catalyzes a key reaction of a methionine salvage pathway, while in green sulfur bacteria, RLP plays a role in oxidative thiosulfate metabolism. In many organisms, the function of RLP is unknown. Indeed, there now appear to be at least six different clades of RLP molecules found in nature. Consideration of the many RubisCO (forms I, II, and III) and RLP (form IV) sequences in the database has subsequently led to a coherent picture of how these proteins may have evolved, with a form III RubisCO arising from theMethanomicrobiaas the most likely ultimate source of all RubisCO and RLP lineages. In addition, structure-function analyses of RLP and RubisCO have provided information as to how the active sites of these proteins have evolved for their specific functions.
Seven genomic subtypes of chronic fatigue syndrome/myalgic encephalomyelitis: a detailed analysis of gene networks and clinical phenotypes
Authors: Kerr J R , Burke B , Petty R , Gough J , Fear D , Mattey D L , Axford J S , Dalgleish A G , Nutt D J 
Published: December 2007

Aim:Chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) is a multisystem disease, the pathogenesis of which remains undetermined. The authors have recently reported a study of gene expression that identified differential expression of 88 human genes in patients with CFS/ME. Clustering of quantitative PCR (qPCR) data from patients with CFS/ME revealed seven distinct subtypes with distinct differences in Medical Outcomes Survey Short Form-36 scores, clinical phenotypes and severity.Methods:In this study, for each CFS/ME subtype, those genes whose expression differed significantly from that of normal blood donors were identified, and then gene interactions, disease associations and molecular and cellular functions of those gene sets were determined. Genomic analysis was then related to clinical data for each CFS/ME subtype.Results:Genomic analysis revealed some common (neurological, haematological, cancer) and some distinct (metabolic, endocrine, cardiovascular, immunological, inflammatory) disease associations among the subtypes. Subtypes 1, 2 and 7 were the most severe, and subtype 3 was the mildest. Clinical features of each subtype were as follows: subtype 1 (cognitive, musculoskeletal, sleep, anxiety/depression); subtype 2 (musculoskeletal, pain, anxiety/depression); subtype 3 (mild); subtype 4 (cognitive); subtype 5 (musculoskeletal, gastrointestinal); subtype 6 (postexertional); subtype 7 (pain, infectious, musculoskeletal, sleep, neurological, gastrointestinal, neurocognitive, anxiety/depression).Conclusion:It was particularly interesting that in the seven genomically derived subtypes there were distinct clinical syndromes, and that those which were most severe were also those with anxiety/depression, as would be expected in a disease with a biological basis.
Inter-relationships between inflammatory markers in patients with stable COPD with bronchitis: intra-patient and inter-patient variability
Authors: Sapey E , Bayley D , Ahmad A , Newbold P , Snell N , Stockley R A 
Published: December 2007

Background:Measurements of pulmonary biomarkers can be used to monitor airway inflammation in chronic obstructive pulmonary disease (COPD), but the variability of sampled biomarkers and their inter-relationships are poorly understood. A study was undertaken to examine the intra- and inter-patient variability in spontaneous sputum samples from patients in the stable state and to describe the relationship between biomarkers, cell counts and markers of disease.Methods:Sputum interleukin-1β, tumour necrosis factor α, interleukin 8, myeloperoxidase, leucotriene B4, growth-related oncogene α and differential cell counts were measured in patients with moderate to severe stable COPD (n = 14) on 11 occasions over a 1-month period.Results:There was significant variability in all inflammatory indices (median intra-patient coefficient of variation (CV) 35% (IQR 22–69), median inter-patient CV 102% (IQR 61–145)). Variability could be reduced by using a rolling mean of individual patient data points. Sample size calculations were undertaken to determine the number of patients required to detect a 50% reduction in neutrophil count. Using a crossover design of a putative effective treatment, the number needed using one data point per patient was 72, reducing to 23 when a mean of three data points was used. Significant correlations were demonstrated both between the inflammatory biomarkers themselves and between inflammatory biomarkers and markers of disease. Some relationships were not apparent when results from a single sample were used. The reliability of inter-relationships improved as more data points were used for each patient.Conclusions:Clear relationships exist between inflammatory biomarkers in patients with stable COPD. Sequential sampling reduced the variability of individual mediators and the potential number of patients needed to power proof of concept interventional studies.
The Khaviz Anticline: an outcrop analogue to giant fractured Asmari Formation reservoirs in SW Iran
Authors: Wennberg O. P. , Azizzadeh M. , Aqrawi A. A. M. , Blanc E. , Brockbank P. , Lyslo K. B. , Pickard N. , Salem L. D. , Svånå T. 
Published: December 2007

Abstract
The carbonate reservoirs in the Late Oligocene—Early Miocene Asmari Formation in the Dezful Embayment of SW Iran are characterized by low matrix permeability, and effective drainage is dependent on the occurrence of open fractures. Limited information on fracture orientation and fracture density is available from core and borehole image data, and high-quality/high-resolution three-dimensional seismic is often lacking in this area. Well and core data do not contain information on important fracture parameters like length distribution, crosscutting relationships, fracture density v. lithology and bed thickness. The understanding of fracture distribution and formation in the region and their effects on fluid flow has been greatly improved by the use of outcrop analogue data. Exposures of the Asmari Formation in the Khaviz Anticline are in close vicinity to the giant hydrocarbon fields. The Khaviz Anticline has a similar geometry and structural history to the major hydrocarbon fields in the area, and represents an excellent analogue for these. Two types of fracture features were observed: diffuse fracturing and fracture swarms. The diffuse fractures form networks and comprise structures grouped into four fractures sets, which are the typical for this type of anticline. Two orthogonal fracture sets are oriented parallel and perpendicular to the fold axis, and two conjugate fracture sets are oblique to the fold axis with their obtuse angle intersecting the trend of the fold axis. The fractures are typically stratabound, sub-perpendicular to bedding and commonly about the bounding stratigraphic surfaces. To a large extent the density and height of fractures in the Asmari Formation are controlled by the mechanical stratigraphy, which is controlled by the depositional environment and cycles. These outcrop data have been essential in the generation of discrete fracture network (DFN) models and the population of the fracture properties in the reservoir models.
Using VSP surveys to bridge the scale gap between well and seismic data
Authors: Emsley S. J. , Shiner P. , Enescu N. , Beccacini A. , Cosma C. 
Published: December 2007

Abstract
This case study was undertaken for a low-porosity fractured carbonate reservoir with a complex fracture network resulting from several phases of tectonic activity. The integration of the image log and seismic-derived interpretations was problematic due to the complexity of the image log signature and the variable quality of the surface seismic data. Earlier experience indicated that VSPs may provide information on faulting and/or fracturing that may otherwise be difficult to determine with confidence from other data sources. Consequently, specialist VSP processing techniques were used to identify and map reflectors in three-dimensional space. Data acquired in two wells were reprocessed to interpret structural features and determine their geometries. The interpreted VSP reflectors were validated and integrated with the analyses of image logs and the interpretation of surface seismic data providing a constrained structural model that allowed the interpretation of seismic data away from well control and provided a starting point for seismic interpretation in areas where structural geometries were poorly imaged on surface seismic. It is shown that VSP, including vertical incidence, data can contribute to the understanding of reservoirs and enables well-derived information to be extrapolated away from the wells.
Study of fracture-induced anisotropy from discrete fracture network simulation of well test responses
Authors: Leckenby R. J. , Lonergan L. , Rogers S. F. , Sanderson D. J. 
Published: December 2007

Abstract
Different conceptualizations of fracture networks have been generated in order to simulate well tests in fractured reservoirs. These models have two purposes: firstly to investigate whether the behaviour of realistic fracture networks can be emulated with more simple models; and secondly to assess whether different sources of anisotropy have characteristic and recognizable influences on the pressure derivative. The anisotropy of the fracture networks was increased by decreasing the angle between two originally orthogonal fracture sets, and by increasing the permeability contrast between two orthogonal fracture sets. Results indicate that simple models can capture the first-order behaviour of more realistic examples. However because early time data are strongly influenced by the connectivity of the fracture network, the degree of anisotropy can only be assessed at later times in a test. Increasing anisotropy results in increasing heterogeneity and compartmentalization, and permeability anisotropy in an orthogonal system can only partially replicate the behaviour of a geometrically anisotropic system.
A surface-subsurface study of reservoir-scale fracture heterogeneities in Cretaceous carbonates, North Oman
Authors: De Keijzer M. , Hillgartner H. , Al Dhahab S. , Rawnsley K. 
Published: December 2007

Abstract
Reservoir-scale structural heterogeneity, especially in terms of mechanical layering and natural fracture systems, is often insufficiently constrained by subsurface data alone. In North Oman, a large dataset in Cretaceous carbonates comprises data from multiple subsurface reservoirs and analogue outcrops. This provides an ideal opportunity to integrate outcrop constraints into the subsurface, and to calibrate the resulting models dynamically. For this purpose, a reservoir-scale analogue outcrop fracture template was created for the Jebel Madmar anticline in the Oman Mountains foothills. The outcrop template provides improved conceptual and quantitative constraints on (i) fracture types and dimensions (e.g. of NE-trending fracture corridors), (ii) fracture heterogeneity, both aerially and stratigraphically, (iii) fracture properties (e.g. cementation evolution, variations due to preferential fault/fracture reactivation) and (iv) structural evolution and history of reactivation. Within a regionally consistent structural framework, the outcrop template has greatly assisted in the creation of geologically realistic models for one of the fractured carbonate reservoirs, complementing the subsurface dataset. Initial dynamic calibration indicates successful application of the outcrop template in that the spatial fracture heterogeneity was succesfuUy captured in the reservoir models and provides a history match to production data. The reduced range of possible fracture system geometries in turn has provided better constraints on the effective fracture properties.
The rediscovery of an ancient exploitation site of Piperno, a valuable historical stone from the Phlegraean Fields (Italy)
Authors: Calcaterra D. , Cappelletti P. , De' Gennaro M. , De Gennaro R. , De Sanctis F. , Flora A. , Langella A. 
Published: December 2007

Abstract
This paper reports the research results over several years on Piperno, the most important ornamental architectural stone of Naples. Particular attention is paid to the rediscovery of the old exploitation sites of this rock and to the survey of the last underground quarry site, still accessible, at the base of the Camaldoli Hill (western Naples) at Pianura. The conservation state was assessed by means of specific surveys in view of possible futu
re utilization. At present, the re-opening of abandoned quarries is not possible owing to unsafe site conditions. The cultural relevance of the Pianura quarry site could suggest its possible restoration as a museum of mining and a centre for teaching the working of ornamental stone within the Campania Region.
Post-depositional modification of atmospheric dust on a granite building in central Rio de Janeiro: implications for surface induration and subsequent stone decay
Authors: Smith B. J. , McAlister J. J. , Baptista Neto J. A. , Silva M. A. M. 
Published: December 2007

Abstract
Extensive contour scaling of a 200 year old granite church is associated with the breaching of an apparently iron-rich crust and the widespread deposition of atmospheric dust within the canyon-like streetscape of Rio de Janeiro. Contemporary dust, accumulated dust from within a depression on the building surface, the surface crust and the underlying granite are examined by a combination of total element analysis and sequential extraction, X-ray diffraction and energy dispersive X-ray fluorescence. Results indicate an increase in total organic carbon and marked decrease in pH within the accumulated dust, and a rapid mobilization of anions and cations from the water-soluble and carbonate phases. It is considered that the latter is linked to salt accumulation within and eventual salt weathering of the granite. Post-depositional alteration of the dust is also linked with the de-silicification of clay minerals (illite to kaolinite) and the loss of silica from the amorphous Fe/Mn phase of the accumulated dust under the initially saline and progressively more acidic conditions experienced at the stone-atmosphere interface. This mobilization of silica is associated with the formation of what is, in effect, a thin silica-rich surface crust or glaze. Within the glaze, accessory amounts of extractable iron are concentrated within the amorphous and crystalline Fe/Mn phases at levels that are significantly elevated with respect to the underlying granite, but much lower than in the equivalent phases of the accumulated dust from which it is principally assumed to derive. The protection afforded to the stonework by the crust is not, however, permanent and within the last 15 years it has been possible to observe a rapid increase in the surface delamination of the church close to street level.
Geomythology: geological origins of myths and legends
Authors: Vitaliano Dorothy B. 
Published: December 2007

Abstract
Myths and geology are related in several ways. Some myths are the result of man's attempts to explain noteworthy features of his environment, such as striking landforms or unusual smaller features, whereas others try to account for conspicuous natural processes, such as earthquakes, volcanic phenomena, and floods. Local myths have sometimes proved helpful in solving geological problems, and even the geological nomenclature is indebted to mythology. Examples of each kind of relationship are given.
Geo-mythology of India
Authors: Chandrasekharam D. 
Published: December 2007

Abstract
In all the Indian legends, whether it is the Ramayana or Mahabharata, one can find embedded elements of geological processes. Perhaps due to the lack of a sound scientific basis for recognizing geological processes in ancient Indian civilization, such processes were believed to be the acts of ‘Gods’ (Suras) and ‘Demons’ (Asuras) and hence they formed an integral part of these legends. Even in the present age where science is able to explain several geological processes, the Hindu faith is such that these myths and legends continue to be passed on to succeeding generations. The fact that these geological processes are contained in these epics helps to sustain truth (dharma) and maintain harmony. Ancient Indian civilization adopted this doctrine and its continuance will remain a fresh and vital part of future generations in India.
The Fenris Wolf in the Nordic Asa creed in the light of palaeoseismics
Authors: Mörner N.-A. 
Published: December 2007

Abstract
The Nordic Asa Creed talks about a giant wolf, ‘the Fenris Wolf’, that was trapped and chained deep in the mountains. When he howled, the ground trembled violently and fractured. With the discovery of frequent high-magnitude palaeoseismic events in Sweden not only in de-glacial time but also in Late Holocene time, it seems both natural and logical that the Fenris tale refers to frightening earthquake events in the past. Once again tales and sagas have been shown to be rooted in facts.
Sooty sweat stains or tourmaline spots? The Argonauts on the Island of Elba (Tuscany) and the spread of Greek trading in the Mediterranean Sea
Authors: Dini Andrea , Corretti Alessandro , Innocenti Fabrizio , Rocchi Sergio , Westerman David Scott 
Published: December 2007

Abstract
In various ancient authors (e.g. the ‘Argonautika’ of Apollonios Rhodios) curious news about the Island of Elba can be found, concerning the existence, somewhere on the shore near Portoferraio, of pebbles that are ‘dirty’ from the Argonauts' sweat. The Argonauts are said to have stopped on the island during their journey back from the looting of the ‘Golden Fleece’. These pebbles are found to be typical of the gravelly beaches below the Capo Bianco cliffs. Such walls are made up of a bony-white aplitic rock dotted with blue-black tourmaline spots. Capo Bianco aplite is the uncommon result of the solidification of a boron-rich magma in a subvolcanic setting. Here, the separation of a boron-rich fluid phase gave way to the crystallization of peculiar spherical dark tourmaline clots in a very fine-grained white groundmass. This rock was noted by Argonauts (i.e. the ancient travellers they represent) and used as a lighthouse to the harbour of Argoos limen (now Portoferraio). Also in the myth, the unique mottled pebbles were recorded as stained by the Argonauts' sweat. The occurrence, within the same, complex myth, of ‘data’ concerning navigation (the white cliffs) and geology (description of the spotted aplite) identify the Argonauts as a blending of mineral prospectors, explorers and early eighteenth century-like naturalists, legitimatizing the commercial/political presence of Greeks in the region.
On the discovery of the ice age: science and myth
Authors: Berger W. H. 
Published: December 2007

Abstract
The discovery of the ice ages began with the invention of the Great Ice Age by Louis Agassiz, in the first half of the nineteenth century. His ideas were shaped by the interpretation of skeletons and frozen remains of large mammals found in Siberia, at the beginning of the nineteenth century. The concept of the Great Ice Age stands in contrast to earlier notions emphasizing widespread flooding, notions that owed much to the Great Flood described in the Bible, and which gave rise to geological terms such as ‘diluvial deposits’ and ‘glacial drift’. Nordic myth as recorded in Iceland during the Middle Ages likewise contains observations and interpretations concerning the remains of giant animals emerging from frozen ground and makes reference to large-scale flooding. The ancient cosmogony related by Icelandic poets postulates the former existence of a kingdom of ice, represented by a primeval Ice Giant, whose rule is ended by the newly emerged gods. According to the myth, the melting of ice (the blood of the dying Giant) caused widespread flooding that killed the large creatures abundant during ice time.
Siluro-Devonian Alpine reefs and pavements
Authors: Hubmann Bernhard , Suttner Thomas 
Published: December 2007

Abstract

Palaeozoic sediments of Austria are separated by the Periadriatic Fault into Eastern Alpine (Upper, Middle and Lower Austroalpine) and Southern Alpine units. We herein present six case studies showing up the different development of shallow-marine communities with special regard to carbonate factories and shell pavements occurring in both regions during the Siluro-Devonian time span. Upper Silurian—Upper Devonian deposits of the Eastern Alps comprise accumulations of serpulid tubes (Southern Burgenland) and
Septatrypa
pavements,
Amphipora
mounds, coral-stromatoporoid—biostromes and
Stachyodes
—auloporoid beds regarded as pioneer reef communities (Graz Palaeozoic), respectively. Lower Silurian strata of the Southern Alps consist of pelagic sediments persisting to the Upper Silurian and therefore differ from contemporaneous successions in the Eastern Alps. Intercalated in Ludlow orthocerid limestone beds
Cardiola
pavements appear (Carnic Alps). Within the Lower Devonian sequence, mounds were built by baffling calcareous algae and tabulozoan communities. Coral-stromatoporoid patch reefs occur during the Pragian, Givetian and Frasnian stages.
Sedimentology and magnetic susceptibility of the Upper Eifelian-Lower Givetian (Middle Devonian) in SW Belgium: insights into carbonate platform initiation
Authors: Mabille Cédric , Boulvain Frédéric 
Published: December 2007

Abstract
The major part of the Hanonet Formation is deposited on a mixed siliciclastic—carbonate detrital ramp, whereas the top is dominated by carbonate-rimmed shelf-related sedimentation. The transition corresponds roughly to the Eifelian—Givetian boundary. This work is based on two stratigraphic sections located in the southern part of the Dinant Synclinorium. Petrographic study leads to the definition of 11 microfacies, which demonstrate important sedimentological differences existing between the sections. A curve showing microfacies evolution is interpreted in terms of changing bathymetry. An environmental model depicts the lateral transition from a multiclinal carbonate ramp (to the east) to a fore-reef setting (to the west). Magnetic susceptibility was used to establish accurate stratigraphic correlations between the two sections. It also leads to an appreciation of the relative importance of eustatic sea-level change and local sedimentation rate. The combined interpretation of the microfacies curves and the magnetic susceptibility provides a new view of the sedimentary dynamics of the studied sections and, in a more general way, a better understanding of the processes responsible for magnetic susceptibility variations in carbonate rocks.