bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Recombination between Human Immunodeficiency Virus Type 1 (HIV-1) and HIV-2, Two Distinct Human Lentiviruses
Authors: Motomura Kazushi , Chen Jianbo , Hu Wei-Shau 
Published: December 2007

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) and HIV-2 are genetically distinct viruses that each can cause AIDS. Approximately 1 million people are infected with both HIV-1 and HIV-2. Additionally, these two viruses use the same receptor and coreceptors and can therefore infect the same target cell populations. To explore potential genetic interactions, we first examined whether RNAs from HIV-1 and HIV-2 can be copackaged into the same virion. We used modified near-full-length viruses that each contained a green fluorescent protein gene (
gfp
) with a different inactivating mutation. Thus, a functional
gfp
could be reconstituted via recombination, which was used to detect the copackaging of HIV-1 and HIV-2 RNAs. The GFP-positive (GFP
+
) phenotype was detected in approximately 0.2% of the infection events, which was 35-fold lower than the intrasubtype HIV-1 rates. We isolated and characterized 54 GFP
+
single-cell clones and determined that all of them contained proviruses with reconstituted
gfp
. We then mapped the general structures of the recombinant viruses and characterized the recombination junctions by DNA sequencing. We observed several different recombination patterns, including those that had crossovers only in
gfp
. The most common hybrid genomes had heterologous long terminal repeats. Although infrequent, crossovers in the viral sequences were also identified. Taken together, our study demonstrates that HIV-1 and HIV-2 can recombine, albeit at low frequencies. These observations indicate that multiple factors are likely to restrict the generation of viable hybrid HIV-1 and HIV-2 viruses. However, considering the large coinfected human population and the high viral load in patients, these rare events could provide the basis for the generation of novel human immunodeficiency viruses.
Functional Analysis of the Murine Cytomegalovirus Chemokine Receptor Homologue M33: Ablation of Constitutive Signaling Is Associated with an Attenuated Phenotype In Vivo
Authors: Case Ruth , Sharp Emma , Benned-Jensen Tau , Rosenkilde Mette M. , Davis-Poynter Nicholas , Farrell Helen E. 
Published: December 2007

ABSTRACTThe murine cytomegalovirus (MCMV) M33 gene is conserved among all betaherpesviruses and encodes a homologue of seven-transmembrane receptors (7TMR) with the capacity for constitutive signaling. Previous studies have demonstrated that M33 is important for MCMV dissemination to or replication within the salivary glands. In this study, we probed N- and C-terminal regions of M33 as well as known 7TMR signature motifs in transmembrane (TM) II and TM III to determine the impact on cell surface expression, constitutive signaling, and in vivo phenotype. The region between amino acids R340and A353of the C terminus was found to be important for CREB- and NFAT-mediated signaling, although not essential for phosphatidylinositol turnover. Tagging or truncation of the N terminus of M33 resulted in loss of cell surface expression. Within TM II, an F79D mutation abolished constitutive signaling, demonstrating a role, as in other cellular and viral 7TMR, of TM II in receptor activation. In TM III, the arginine (but not the asparagine) residue of the NRY motif (the counterpart of the common DRY motif in cellular 7TMR) was found to be essential for constitutive signaling. Selected mutations incorporated into recombinant MCMV showed that disruption of constitutive signaling for a viral 7TMR homologue resulted in a reduced capacity to disseminate to or replicate in the salivary glands. In addition, HCMV UL33 was found to partially compensate for the lack of M33 in vivo, suggesting conserved biological roles of the UL33 gene family.
Are relay ramps conduits for fluid flow? Structural analysis of a relay ramp in Arches National Park, Utah
Authors: Rotevatn Atle , Fossen Haakon , Hesthammer Jonny , Aas Tor E. , Howell John A. 
Published: December 2007

Abstract
Relay ramps associated with overlapping faults are commonly regarded as efficient conduits for fluid flow across potentially sealing intra-reservoir fault zones. The current study demonstrates that structural heterogeneity in the often anomalously wide damage zone of relay ramps may represent potential baffles to intra-ramp fluid flow. A network of ramp-parallel, ramp-diagonal and curved cataclastic deformation bands causes compartmentalization of the ramp studied in Arches National Park, Utah. Harmonic average calculations demonstrate that, although single deformation bands have little or no effect on effective permeability, the presence of even a very small number of low-permeable deformation band clusters could reduce along-ramp effective permeability by more than three orders of magnitude. Thus, although relay zones may maintain large-scale geometric communication, the results of this study demonstrate that caution must be exercised when considering relay ramps as fluid conduits across sealing faults in a production situation. Although relay ramps clearly represent effective migration pathways for hydrocarbons over geological time, the extent to which they conduct fluids in a production situation is more uncertain. Quantitative approaches include adjusting the transmissibility multipliers for faults in reservoir models to allow for increased cross-fault flow. If, however, the effect of internal structural heterogeneity is not taken into consideration, this type of adjustment may lead to gross overestimation of the effect of relay ramps. Sedimentology, stratigraphy, burial history and deformation mechanisms are some of the controlling factors for the formation of such structural heterogeneities.
The scaling of fracture compliance
Authors: Worthington M. H. , Lubbe R. 
Published: December 2007

Abstract

The seismic visibility of fractures depends on the magnitude of their normal and shear compliance and how these quantities vary with the scale of the fracture and depth of burial. Reliable estimates of fracture compliance as a function of confining pressure, in the range 10
-13
–10
-14
m Pa
-1
, have been obtained from laboratory measurements on core samples. The possibility of fractal scaling of fracture parameters has been proposed, in which case fracture compliance might be expected to increase with the scale of the fracture. Laboratory and field estimates of fracture compliance are presented covering a range of fracture sizes. Compliance is shown to increase with the scale of the fractures. Results obtained are broadly consistent with the magnitudes predicted from linear slip theory, in which the displacement discontinuity across a partially sealed interface is linearly related to the traction on the interface.
The Machar Oil Field: waterflooding a fractured chalk reservoir
Authors: Casabianca D. , Jolly R. J. H. , Pollard R. 
Published: December 2007

Abstract
The Machar Oil Field is a fractured Chalk Group reservoir, of Late Cretaceous age, developed above a salt diapir in the Central Graben of the UK Continental Shelf. From 1998 to the present the field has been produced through a water injection scheme sanctioned on the basis of data acquired during a water injection pilot test carried out in 1996. After three years of strong production, performance was affected by an unexpectedly fast rise in water-cut. This prompted the field management team to review the available data and rebuild the reservoir model to serve as the basis for a revised development plan. This paper describes the data used and the lines of evidence followed by the team in order to identify, describe and model the key subsurface characteristics, and related uncertainties, controlling field behaviour and impacting reservoir management and development options. Key uncertainties are the nature and flow significance of an extensive network of faults, the presence, nature and significance of a system of sub-seismic background fractures and the role played by the matrix capillary and wettability properties in controlling recovery through imbibition levels and rates. The successful integration of a wide range of subsurface static data, such as biostratigraphy, fracture identification, stress identification, seismic fault mapping and dynamic data, such as production logs, pressure build-up tests and tracer recovery, resulted in improved reservoir characterization. The ensuing new reservoir model explained the field historic performance and suggested two redevelopment options, which were sanctioned and executed between 2003 and 2004, and resulted in improved field performance.
Integrating discrete fracture network models and pressure transient data for testing conceptual fracture models of the Valhall chalk reservoir, Norwegian North Sea
Authors: Rogers S. , Enachescu C. , Trice R. , Buer K. 
Published: December 2007

Abstract
The Valhall Field is an Upper Cretaceous chalk reservoir located in the Central Graben area of the North Sea with production coming from the fractured Tor and Hod formations. Well tests and production history indicate that these formations are highly heterogeneous and that significant fluid flow occurs through both the matrix and fracture system. However there remained significant uncertainty about the specific controls and location of the main productivity conduits and how they would influence sweep efficiency during planned water flood. To address these uncertainties a range of possible conceptual fracture models were considered with respect to controls on major flow within the reservoir. Analysis indicated that the reservoir is dominated by a connected series of seismic scale faults acting as major flow conduits with smaller fractures providing a less significant enhancement to matrix permeability. A key input to this study was the examination of over 80 well tests. Simulation of a number of key well tests using a simple discrete fracture network model comprising a connected fault network and pseudo-matrix layer was able to reproduce the majority of the observed pressure derivative shapes. This gave some confidence to the understanding of major reservoir flow paths as well as providing calibrated fault properties for direct inclusion within the simulation model.
Characterizing fracture and matrix heterogeneities in folded Devonian carbonate thrust sheets, Waterton tight gas fields, Western Canada
Authors: Rawnsley K. , De Keijzer M. , Wei L. , Bettembourg S. , Asyee W. , Massaferro J.-L. , Swaby P. , Drysdale D. , Boettcher D. 
Published: December 2007

Abstract
Well performance is extremely variable in the stacked sequence of relatively tight Devonian and Mississippian carbonates in the northern part of the Waterton Complex, Alberta, Canada. This is despite having an extensively developed fracture system present in all the wells. In order to determine why some wells penetrated more permeable fractures than others, a full reinterpretation of the geophysical, structural, stress, matrix and dynamic data sets was carried out. Flow simulations at sector scales using discrete fracture network models and fullfield continuum modelling were used to test a range of geological and dynamic scenarios. One of the most northwestern fields of the Waterton complex, the West Carbondale field, is the focus of the work presented. For this field the best-fit dynamic models consist of a major fracture zone, corresponding to either a seismic scale lineament or zone of enhanced curvature, trending through the area of most prolific wells. Outside this zone, the vast majority of the fracture system makes little contribution to the flow in the wells, other than slightly enhancing the reservoir permeability.
Diagnosing decay: the value of medical analogy in understanding the weathering of building stones
Authors: Smith B. J. , Přikryl R. 
Published: December 2007

Abstract
This paper represents the first element of the introduction to this volume, and as such investigates its principal underlying rationale; namely the importance of accurate diagnosis of stone decay in the formulation of effective conservation strategies. It does this by exploring ways in which perceived similarities between stone decay and human disease have influenced attitudes towards conservation, and how refinements within medical diagnostic strategies can inform future condition assessments of building stones. In doing so, it identifies the importance of looking beyond obvious symptoms to the isolation of the fundamental causes of decay and the factors that control them. These controls are strongly conditioned by accumulated stresses within the stonework. In many buildings these are the product of a complex history involving exposure to a variety of environmental conditions and successive human intervention. Only by understanding these memory effects is it possible to explain current decay phenomena, attempt any prediction of future behaviour or recommend appropriate intervention. The concept of appropriateness is further developed through an examination of the TNM (Tumours, Nodes and Metastases) Staging System for cancer diagnosis. This holistic scheme embodies a progressive approach to diagnosis that begins with a clinical assessment based on how the patient presents, and leads on to more detailed pathological investigations involving sampling, testing and analysis. The scheme also requires an assessment of the certainty of the diagnosis and proposed treatments must be viewed in terms of a cost benefit analysis. A modified version of this staging system has already been developed for use in the physical assessment of buildings. It is suggested that the next stage in its development, and that of any other condition assessment procedure that deals solely with the fabric of a building, is the inclusion of a value-based appraisal of its cultural significance.
Natural stone portals of the town of Udine (Italy): their design, construction and materials between the 15th and 20th centuries
Authors: Frangipane Anna 
Published: December 2007

Abstract
The research focuses on the features of 250 natural stone portals of the civil buildings of the town of Udine (NE Italy), dating between the 15th and 20th centuries. In order to clearly define the number, characteristics and uniqueness of these architectural elements, three strategies were implemented: (i) a concise database of all the portals; (ii) a concise reference database of more than 100 portals of five significant nearby towns; and (iii) a detailed inventory, consisting of data and photographs of about 200 portals selected for relevance or because they represent a recurrent type. The analysis of the data collected, supported by reference studies of quarry location, stone-cutter activity, the work of architects, cultural relationships with immediate and distant influences permitted the definition of an interdisciplinary framework describing the main features of portal production, as related to formal evidence, stone materials, historical building and carving techniques. The rational organization of the huge set of data collected represents an effective working tool, interconnecting different aspects of the portals' realization, which was indispensable for the research, but will also be useful for further research on the role of stone material in the historic buildings of Udine.
The dimension stone potential of Thailand — overview and granite site investigations
Authors: Hoffmann A. , Siegesmund S. 
Published: December 2007

Abstract
The production of dimension stones is well established in Thailand and the country has considerable processing capacities in the region, second only to China. The geological background of Thailand provides a huge potential of dimension stones, including magmatic, metamorphic and sedimentary rocks. The NE part of the country is made up by the Khorat Plateau with the main sandstone resources at its western margin. Metamorphic carbonate rocks are predominantly distributed along the border of a basin area in central Thailand. The western part of the country is characterized by magmatic belts that comprise the resources of igneous rocks. Large quantities of the dimension stone potential were used in the first part of the 1990s, when the domestic economy underwent a considerable upturn. The most important region for the production of granitoid rocks is the Tak batholith in northern Thailand. Therefore, the Tak granitoids are discussed as a case study with respect to petrophysical and depositional characteristics.
Photo-based decay mapping of replaced stone blocks on the boundary wall of Worcester College, Oxford
Authors: Thornbush M. J. , Viles H. A. 
Published: December 2007

Abstract

In this study on the boundary wall of Worcester College, Oxford, the decay mapping in Adobe Photoshop (DMAP) approach is introduced to test the use of simple daylight photographs in the long-term monitoring of stone decay. This is conducted primarily through measured changes in surface brightness and roughness based on close-up photographic images of walls. The Magic Wand Tool was applied to greyscale images in Lab Color Mode to select proportions of pixels with a lightness (
L
) value of 77%. This paper shows the effectiveness of the calibration procedure used to validate lightness between surveys so that cross-temporal comparisons have a greater validity. It also outlines and discusses errors associated with the method as well as its limitations. The DMAP approach proves to be particularly useful when applied to long-term monitoring exceeding 5 years of survey.
The weathering and weatherability of Basílica da Estrela stones, Lisbon, Portugal
Authors: Figueiredo C. A. M. , Aires-Barros L. , Basto M. J. , Graça R. C. , Maurício A. 
Published: December 2007

Abstract
This paper presents a study of stone decay on the Basílica da Estrela, the most famous 18th century monument in the city of Lisbon, Portugal. It was built with Jurassic and Cretaceous limestones from the surroundings of Lisbon. Different approaches were used to establish the typology, causes and processes of the major weathering forms. Limestone samples from ancient quarries, salt efflorescences and disintegrated stone material from the interior of the church were characterized by chemical, mineralogical and petrographical analyses. Limestone physical properties related to fluid percolation were also determined. Detailed surveys of stone decay phenomena were carried out on the monument. Textures of grey-level images representative of the weathering forms were analysed by image analysis through covariance and granulometry operators. An HIDSPEC computational hydrogeochemical model, phase and graphical diagrams, and multivariate statistical analysis were used for water-rock interaction studies. Physical weathering forms prevail inside the church. The yellow Cretaceous limestone is the most deteriorated stone. This observation compares well with its intrinsic properties. The weathering is determined by the stone structures, such as stilolytes and fossils, and architectural features (geometry and surface finish). Soluble salts such as trona and thenardite were only found in a very small area inside the church.
The mineralogical and chemical methods in investigations of decay of the Devonian black ‘marble’ from Debnik (Southern Poland)
Authors: Marszałek M. 
Published: December 2007

Abstract
Optical microscopy, scanning electron microscopy with energy dispersive spectrometry, X-ray diffraction, infrared (IR) spectroscopy, Rock-Eval pyrolysis and gas chromatography combined with mass spectroscopy were used to examine deterioration of the black limestone from Dębnik near Cracow. Owing to its unique colour and good polishing properties the rock is called the ‘Debnik marble’. The samples were taken from various monuments and natural outcrops exposed to weathering. The material is a compact limestone whose black colour is caused by an admixture of bitumens or pyrite. Its horizontal layers are separated by discontinuities filled with clay minerals. Surface exfoliation is one of the damage signs and results in the formation of irregular or lensoidal fractures. The discontinuities provide an easy access for acid rain that in reaction with calcite produces gypsum.
Crystallization of gypsum leads to alveolar weathering, cracking and chipping of the otherwise compact material. The presence of alveoles or surface exfoliation depends on the orientation of stone blocks. When they are cut along the discontinuities, destruction results in exfoliating and cracking. Perpendicular cutting gives rise to the formation of alveoles. The changes affect the original black colour of the stone surface that alters to grey or even white.
Modelling of the calcareous stone sulphation in polluted atmosphere after exposure in the field
Authors: Lefèvre R.-A. , Ionescu A. , Ausset P. , Chabas A. , Girardet F. , Vince F. 
Published: December 2007

Abstract
Parisian Lutetian and Val-de-Loire Turonian Richemont limestone tablets were exposed, sheltered and unsheltered from rain, for up to 3 years in Paris and Tours, respectively. Sulphur concentrations below the stone surfaces were measured from powders obtained by milling the stone in successive steps of 0.1 mm. In tablets exposed to rain, measured sulphur concentration remains equal to the stone background concentration, implying that the sulphur deposited between rain events is leached by the next event. In contrast, in tablets sheltered from rain, the sulphur concentration in the first layer below the stone surface increases non-linearly with time. Sulphation does not, however, penetrate more than 0.2 mm. A sigmoidal Hill curve provides a good fit with changes in measured sulphur concentration over time within the first layer of each sheltered stone. This model reveals a cumulative phenomenon of sulphation, characterized by a saturation level that obstructs deeper penetration of sulphur within the stone. The model shows the same type of time evolution of sulphation for both stones, but with different coefficients; these coefficients are related to the atmospheric environment of exposure and to the different intrinsic properties of each stone.