Holism and structural realism

We first introduce structural realism as a position in the metaphysics of science, pointing out the way in which this position replaces intrinsic properties with relations so that it amounts to a holistic in contrast to an atomistic metaphysics. We argue in favour of a moderate version of structural realism that puts objects and relations on the same ontological footing and assess the general philosophical arguments for this position. The second section shows how structural realism gains support from quantum physics. The third section explains how structural realism can be applied to the metaphysics of space-time.

Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima.

Studies of the structural basis of protein thermostability have produced a confusing picture. Small sets of proteins have been analyzed from a variety of thermophilic species, suggesting different structural features as responsible for protein thermostability. Taking advantage of the recent advances in structural genomics, we have compiled a relatively large protein structure dataset, which was constructed very carefully and selectively; that is, the dataset contains only experimentally determined structures of proteins from one specific organism, the hyperthermophilic bacterium Thermotoga maritima, and those of close homologs from mesophilic bacteria. In contrast to the conclusions of previous studies, our analyses show that oligomerization order, hydrogen bonds, and secondary structure play minor roles in adaptation to hyperthermophily in bacteria. On the other hand, the data exhibit very significant increases in the density of salt-bridges and in compactness for proteins from T.maritima. The latter effect can be measured by contact order or solvent accessibility, and network analysis shows a specific increase in highly connected residues in this thermophile. These features account for changes in 96% of the protein pairs studied. Our results provide a clear picture of protein thermostability in one species, and a framework for future studies of thermal adaptation.

Structural abnormalities in the thalamus of migraineurs with aura: a multiparametric study at 3 T.

BACKGROUND AND OBJECTIVES: The thalamus exerts a pivotal role in pain processing and cortical excitability control, and migraine is characterized by repeated pain attacks and abnormal cortical habituation to excitatory stimuli. This work aimed at studying the microstructure of the thalamus in migraine patients using an innovative multiparametric approach at high-field magnetic resonance imaging (MRI). DESIGN: We examined 37 migraineurs (22 without aura, MWoA, and 15 with aura, MWA) as well as 20 healthy controls (HC) in a 3-T MRI equipped with a 32-channel coil. We acquired whole-brain T1 relaxation maps and computed magnetization transfer ratio (MTR), generalized fractional anisotropy, and T2* maps to probe microstructural and connectivity integrity and to assess iron deposition. We also correlated the obtained parametric values with the average monthly frequency of migraine attacks and disease duration. RESULTS: T1 relaxation time was significantly shorter in the thalamus of MWA patients compared with MWoA (P < 0.001) and HC (P ≤ 0.01); in addition, MTR was higher and T2* relaxation time was shorter in MWA than in MWoA patients (P < 0.05, respectively). These data reveal broad microstructural alterations in the thalamus of MWA patients compared with MWoA and HC, suggesting increased iron deposition and myelin content/cellularity. However, MWA and MWoA patients did not show any differences in the thalamic nucleus involved in pain processing in migraine. CONCLUSIONS: There are broad microstructural alterations in the thalamus of MWA patients that may underlie abnormal cortical excitability control leading to cortical spreading depression and visual aura.

A structural MRI study of motor conversion disorder: evidence of reduction in thalamic volume.

OBJECTIVE: To investigate potential abnormalities in subcortical brain structures in conversion disorder (CD) compared with controls using a region of interest (ROI) approach. METHODS: Fourteen patients with motor CD were compared with 31 healthy controls using high-resolution MRI scans with an ROI approach focusing on the basal ganglia, thalamus and amygdala. Brain volumes were measured using Freesurfer, a validated segmentation algorithm. RESULTS: Significantly smaller left thalamic volumes were found in patients compared with controls when corrected for intracranial volume. These reductions did not vary with handedness, laterality, duration or severity of symptoms. CONCLUSIONS: These differences may reflect a primary disease process in this area or be secondary effects of the disorder, for example, resulting from limb disuse. Larger, longitudinal structural imaging studies will be required to confirm the findings and explore whether they are primary or secondary to CD.

Structural determinants involved in the activation and regulation of G protein-coupled receptors: lessons from the alpha1-adrenegic receptor subtypes.

The aim of a large number of studies on G protein-coupled receptors was centered on understanding the structural basis of their main functional properties. Here, we will briefly review the results obtained on the alpha1-adrenergic receptor subtypes belonging to the rhodopsin-like family of receptors. These findings contribute, on the one hand, to further understand the molecular basis of adrenergic transmission and, on the other, to provide some generalities on the structure-functional relationship of G protein-coupled receptors.

Automatic quality assessment in structural brain magnetic resonance imaging

MRI has evolved into an important diagnostic technique in medical imaging. However, reliability of the derived diagnosis can be degraded by artifacts, which challenge both radiologists and automatic computer-aided diagnosis. This work proposes a fully-automatic method for measuring image quality of three-dimensional (3D) structural MRI. Quality measures are derived by analyzing the air background of magnitude images and are capable of detecting image degradation from several sources, including bulk motion, residual magnetization from incomplete spoiling, blurring, and ghosting. The method has been validated on 749 3D T(1)-weighted 1.5T and 3T head scans acquired at 36 Alzheimer's Disease Neuroimaging Initiative (ADNI) study sites operating with various software and hardware combinations. Results are compared against qualitative grades assigned by the ADNI quality control center (taken as the reference standard). The derived quality indices are independent of the MRI system used and agree with the reference standard quality ratings with high sensitivity and specificity (>85%). The proposed procedures for quality assessment could be of great value for both research and routine clinical imaging. It could greatly improve workflow through its ability to rule out the need for a repeat scan while the patient is still in the magnet bore.

Structural analysis of Turtle Mountain: Origin and influence of fractures in the development of rock slope failures

Large slope failures in fractured rocks are often controlled by the combination of pre-existing tectonic fracturing and brittle failure propagation in the intact rock mass during the pre-failure phase. This study focuses on the influence of fold-related fractures and of post-folding fractures on slope instabilities with emphasis on Turtle Mountain, located in SW Alberta (Canada). The structural features of Turtle Mountain, especially to the south of the 1903 Frank Slide, were investigated using a high-resolution digital elevation model combined with a detailed field survey. These investigations allowed the identification of six main discontinuity sets influencing the slope instability and surface morphology. According to the different deformation phases affecting the area, the potential origin of the detected fractures was assessed. Three discontinuity sets are correlated with the folding phase and the others with post-folding movements. In order to characterize the rock mass quality in the different portions of the Turtle Mountain anticline, the geological strength index (GSI) has been estimated. The GSI results show a decrease in rock mass quality approaching the fold hinge area due to higher fracture persistence and higher weathering. These observations allow us to propose a model for the potential failure mechanisms related to fold structures.

Melt/peridotite interaction in the Southern Lanzo peridotite: Field, textural and geochemical evidence

This paper presents field, petrographic-structural and geochemical data on spinet and plagioclase peridotites from the southern domain of the Lanzo ophiolitic peridotite massif (Western Alps). Spinet lherzolites, harzburgites and dunites crop out at Mt. Arpone and Mt. Musine. Field evidence indicates that pristine porphyroclastic spinet lherzolites are transformed to coarse granular spinet harzburgites, which are in turn overprinted by plagioclase peridotites, while strongly depleted spinet harzburgite and dunite bands and bodies replace the plagioclase peridotites. On the northern flank of Mt. Arpone, deformed, porphyroclastic (lithospheric) lherzolites, with diffuse pyroxenite banding, represent the oldest spinel-facies rocks. They show microstructures of a composite subsolidus evolution, suggesting provenance from deeper (asthenospheric) mantle levels and accretion to the lithosphere. These protoliths are locally transformed to coarse granular (reactive) spinet harzburgites and dunites, which show textures reminiscent of melt/rock reaction and geochemical characteristics suggesting that they are products of peridotite interaction with reactively percolating melts. Geochemical data and modelling suggest that <1-5% fractional melting of spinel-facies DMM produced the injected melts. Plagioclase peridotites are hybrid rocks resulting from pre-existing spinet peridotites and variable enrichment of plagioclase and micro-gabbroic material by percolating melts. The impregnating melts attained silica-saturation, as testified by widespread orthopyroxene replacement of olivine, during open system migration in the lithosphere. At Mt. Musine, coarse granular spinet harzburgite and dunite bodies replace the plagioclase peridotites. Most of these replacive, refractory peridotites have interstitial magmatic clinopyroxene with trace element compositions in equilibrium with MORB, while some Cpx have REE-depleted patterns suggesting transient geochemical features of the migrating MORB-type melts, acquired by interaction with the ambient plagioclase peridotite. These replacive spinet harzburgite and dunite bodies are interpreted as channels exploited for focused and reactive migration of silica-undersaturated melts with aggregate MORB compositions. Such melts were unrelated to the silica-saturated melts that refertilized the pre-existing plagioclase peridotites. Finally, MORB melt migration occurred along open fractures, now recorded as gabbroic dikes. Our data document the complexity of rock-types and mantle processes in the South Lanzo peridotite massif and describe a composite tectonic and magmatic scenario that is not consistent with the ``asthenospheric scenario'' proposed by previous authors. We envisage a ``transitional scenario'' in which extending subcontinental lithospheric mantle was strongly modified (both depleted and refertilized) by early melts with MORB-affinity formed by decompression partial melting of the upwelling asthenosphere, during pre-oceanic rifting and lithospheric thinning in the Ligurian Tethys realm. (C) 2006 Elsevier B.V. All rights reserved.

Hepatitis C virus RNA replication requires a conserved structural motif within the transmembrane domain of the NS5B RNA-dependent RNA polymerase.

Hepatitis C virus (HCV) nonstructural protein 5B (NS5B), the viral RNA-dependent RNA polymerase (RdRp), is a tail-anchored protein with a highly conserved C-terminal transmembrane domain (TMD) that is required for the assembly of a functional replication complex. Here, we report that the TMD of the HCV RdRp can be functionally replaced by a newly identified analogous membrane anchor of the GB virus B (GBV-B) NS5B RdRp. Replicons with a chimeric RdRp consisting of the HCV catalytic domain and the GBV-B membrane anchor replicated with reduced efficiency. Compensatory amino acid changes at defined positions within the TMD improved the replication efficiency of these chimeras. These observations highlight a conserved structural motif within the TMD of the HCV NS5B RdRp that is required for RNA replication.

Structural macro factors and the affine term structure of interest rates

This work consists of three essays investigating the ability of structural macroeconomic models to price zero coupon U.S. government bonds. 1. A small scale 3 factor DSGE model implying constant term premium is able to provide reasonable a fit for the term structure only at the expense of the persistence parameters of the structural shocks. The test of the structural model against one that has constant but unrestricted prices of risk parameters shows that the exogenous prices of risk-model is only weakly preferred. We provide an MLE based variance-covariance matrix of the Metropolis Proposal Density that improves convergence speeds in MCMC chains. 2. Affine in observable macro-variables, prices of risk specification is excessively flexible and provides term-structure fit without significantly altering the structural parameters. The exogenous component of the SDF is separating the macro part of the model from the term structure and the good term structure fit has as a driving force an extremely volatile SDF and an implied average short rate that is inexplicable. We conclude that the no arbitrage restrictions do not suffice to temper the SDF, thus there is need for more restrictions. We introduce a penalty-function methodology that proves useful in showing that affine prices of risk specifications are able to reconcile stable macro-dynamics with good term structure fit and a plausible SDF. 3. The level factor is reproduced most importantly by the preference shock to which it is strongly and positively related but technology and monetary shocks, with negative loadings, are also contributing to its replication. The slope factor is only related to the monetary policy shocks and it is poorly explained. We find that there are gains in in- and out-of-sample forecast of consumption and inflation if term structure information is used in a time varying hybrid prices of risk setting. In-sample yield forecast are better in models with non-stationary shocks for the period 1982-1988. After this period, time varying market price of risk models provide better in-sample forecasts. For the period 2005-2008, out of sample forecast of consumption and inflation are better if term structure information is incorporated in the DSGE model but yields are better forecasted by a pure macro DSGE model.

Multi-source composite kernels for urban image classification

This letter presents advanced classification methods for very high resolution images. Efficient multisource information, both spectral and spatial, is exploited through the use of composite kernels in support vector machines. Weighted summations of kernels accounting for separate sources of spectral and spatial information are analyzed and compared to classical approaches such as pure spectral classification or stacked approaches using all the features in a single vector. Model selection problems are addressed, as well as the importance of the different kernels in the weighted summation.

Le Briançonnais, terrain exotique dans les Alpes ?

New reconstructions of the Western Alps from late Early Jurassic till early Tertiary are proposed. These reconstructions use deep lithospheric data gathered through recent seismic surveys and tomographic studies carried out in the Alps. The present day position, under the Po plain, of the southern limit of the European plate (fig. 1), allows to define the former geometry of the Brianconnais peninsula. The Brianconnais domain is regarded as an exotic terrane formerly belonging to the European margin until Late Jurassic, then transported eastward during the drift of Iberia (fig. 5). Therefore, on a present day Western Alps cross section, a duplication of the European continental margin can be recognized (fig. 10). Stratigraphic and sedimentological data along a zone linking the Pyrenean fracture zone to the Brianconnais, can be related to a rifting event starting in Oxfordian time. This event is responsible for the Late Jurassic till mid-Cretaceous drift of Iberia opening, first the northern Atlantic, then the Gulf of Biscay. Simultaneously, the drift of the Brianconnais will open the Valais ocean and close the Piemontese ocean. The resulting oblique collision zone between the Brianconnais and the Apulian margin generates HP/LT metamorphism starting in Early Cretaceous. The eastward drift of the Brianconnais peninsula will eventually bring it in front of a more northerly segment of the former European margin. The thrusting of the Brianconnais unto that margin takes place in early Tertiary (fig. 9), following the subduction of the Valais ocean. The present nappe pile results not only from continent/continent frontal collision, but also from important lateral displacement of terranes, the most important one being the Brianconnais. The dilemma of `'en echelon'' oceanic domains in the Alps is an outcome of these translations. A solution is found when considering the opening of a Cretaceous Valais ocean across the European margin, running out eastward into the Piemontese ocean, where the drift is taken up along a former transform fault and compensated by subduction under the Apulian margin (fig. 8). In the Western Alps we are then dealing with two oceans, the Piemontese and the Valaisan and a duplicated European margin. In the Eastern Alps the single Piemontese ocean is cut by newly created oceanic crust. All these elements will be incorporated into the Penninic structural domain which does not represent a former unique paleogeographic area, it is a composite accretionary domain squeezed between Europe and Apulia.

Structural analysis, clay mineralogy and K-Ar dating of fault gouges from Centovalli Line (Central Alps) for reconstruction of their recent activity

Between the cities of Domodossola and Locarno, the complex ``Centovalli Line'' tectonic zone of the Central Alps outlines deformation phases over a long period of time (probably starting similar to 30 Ma ago) and under variable P-T conditions. The last deformation phases developed gouge-bearing faults with a general E-W trend that crosscuts the roots of the Alpine Canavese zone and the Finero ultramafic body. Kinematic indicators show that the general motion was mainly dextral associated with back thrusting towards the S. The <2 mu m clay fractions of fault gouges from Centovalli Line consist mainly of illite, smectite and chlorite with varied illite-smectite, chlorite-smectite and chlorite-serpentine mixed-layers. Constrained with the illite crystallinity index, the thermal conditions induced by the tectonic activity show a gradual trend from anchizonal to diagenetic conditions. The <2 and <0.2 mu M clay fractions, and hydrothermal K-feldspar separates all provide K-Ar ages between 14.2 +/- 2.9 Ma and roughly 0 Ma, with major episodes at about 12,8, 6 and close to 0 Ma These ages set the recurrent tectonic activity and the associated fluid circulations between Upper Miocene and Recent. On the basis of the K-Ar ages and with a thermal gradient of 25-30 degrees C/km, the studied fault zones were located at a depth of 4-7 km. If they were active until now as observed in field, the exhumation was approximately 2.5-3.0 km for the last 12 Ma with a mean velocity of 0.4 mm/y. Comparison with available models on the recent Alpine evolution shows that the tectonic activity in the area relates to a continuum of the back-thrusting movements of the Canavese Line, and/or to several late-extensional phases of the Rhone-Simplon line. The Centovalli-Val Vigezzo zone therefore represents a major tectonic zone of the Central-Western Alps resulting from different interacting tectonic events. (C) 2011 Elsevier B.V. All rights reserved.

Survey of prenatal screening policies in Europe for structural malformations and chromosome anomalies, and their impact on detection and termination rates for neural tube defects and Down's syndrome.

OBJECTIVE: To 'map' the current (2004) state of prenatal screening in Europe. DESIGN: (i) Survey of country policies and (ii) analysis of data from EUROCAT (European Surveillance of Congenital Anomalies) population-based congenital anomaly registers. SETTING: Europe. POPULATION: Survey of prenatal screening policies in 18 countries and 1.13 million births in 12 countries in 2002-04. METHODS: (i) Questionnaire on national screening policies and termination of pregnancy for fetal anomaly (TOPFA) laws in 2004. (ii) Analysis of data on prenatal detection and termination for Down's syndrome and neural tube defects (NTDs) using the EUROCAT database. MAIN OUTCOME MEASURES: Existence of national prenatal screening policies, legal gestation limit for TOPFA, prenatal detection and termination rates for Down's syndrome and NTD. RESULTS: Ten of the 18 countries had a national country-wide policy for Down's syndrome screening and 14/18 for structural anomaly scanning. Sixty-eight percent of Down's syndrome cases (range 0-95%) were detected prenatally, of which 88% resulted in termination of pregnancy. Eighty-eight percent (range 25-94%) of cases of NTD were prenatally detected, of which 88% resulted in termination. Countries with a first-trimester screening policy had the highest proportion of prenatally diagnosed Down's syndrome cases. Countries with no official national Down's syndrome screening or structural anomaly scan policy had the lowest proportion of prenatally diagnosed Down's syndrome and NTD cases. Six of the 18 countries had a legal gestational age limit for TOPFA, and in two countries, termination of pregnancy was illegal at any gestation. CONCLUSIONS: There are large differences in screening policies between countries in Europe. These, as well as organisational and cultural factors, are associated with wide country variation in prenatal detection rates for Down's syndrome and NTD.