SIMSAFADIM-CLASTIC: A new approach to mathematical 3D forward simulation modelling for terrigenous and carbonate marine sedimentation

Most sedimentary modelling programs developed in recent years focus on either terrigenous or carbonate marine sedimentation. Nevertheless, only a few programs have attempted to consider mixed terrigenous-carbonate sedimentation, and most of these are two-dimensional, which is a major restriction since geological processes take place in 3D. This paper presents the basic concepts of a new 3D mathematical forward simulation model for clastic sediments, which was developed from SIMSAFADIM, a previous 3D carbonate sedimentation model. The new extended model, SIMSAFADIM-CLASTIC, simulates processes of autochthonous marine carbonate production and accumulation, together with clastic transport and sedimentation in three dimensions of both carbonate and terrigenous sediments. Other models and modelling strategies may also provide realistic and efficient tools for prediction of stratigraphic architecture and facies distribution of sedimentary deposits. However, SIMSAFADIM-CLASTIC becomes an innovative model that attempts to simulate different sediment types using a process-based approach, therefore being a useful tool for 3D prediction of stratigraphic architecture and facies distribution in sedimentary basins. This model is applied to the neogene Vallès-Penedès half-graben (western Mediterranean, NE Spain) to show the capacity of the program when applied to a realistic geologic situation involving interactions between terrigenous clastics and carbonate sediments.

Issue of time in generally covariant theories and the Komar-Bergmann approach to observables in general relativity

Diffeomorphism-induced symmetry transformations and time evolution are distinct operations in generally covariant theories formulated in phase space. Time is not frozen. Diffeomorphism invariants are consequently not necessarily constants of the motion. Time-dependent invariants arise through the choice of an intrinsic time, or equivalently through the imposition of time-dependent gauge fixation conditions. One example of such a time-dependent gauge fixing is the Komar-Bergmann use of Weyl curvature scalars in general relativity. An analogous gauge fixing is also imposed for the relativistic free particle and the resulting complete set time-dependent invariants for this exactly solvable model are displayed. In contrast with the free particle case, we show that gauge invariants that are simultaneously constants of motion cannot exist in general relativity. They vary with intrinsic time.

Dynamical Systems approach to Saffman-Taylor fingering. A Dynamical Solvability Scenario

A dynamical systems approach to competition of Saffman-Taylor fingers in a Hele-Shaw channel is developed. This is based on global analysis of the phase space flow of the low-dimensional ordinary-differential-equation sets associated with the classes of exact solutions of the problem without surface tension. Some simple examples are studied in detail. A general proof of the existence of finite-time singularities for broad classes of solutions is given. Solutions leading to finite-time interface pinchoff are also identified. The existence of a continuum of multifinger fixed points and its dynamical implications are discussed. We conclude that exact zero-surface tension solutions taken in a global sense as families of trajectories in phase space are unphysical because the multifinger fixed points are nonhyperbolic, and an unfolding does not exist within the same class of solutions. Hyperbolicity (saddle-point structure) of the multifinger fixed points is argued to be essential to the physically correct qualitative description of finger competition. The restoring of hyperbolicity by surface tension is proposed as the key point to formulate a generic dynamical solvability scenario for interfacial pattern selection.

TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.

TCRep 3D is an automated systematic approach for TCR-peptide-MHC class I structure prediction, based on homology and ab initio modeling. It has been considerably generalized from former studies to be applicable to large repertoires of TCR. First, the location of the complementary determining regions of the target sequences are automatically identified by a sequence alignment strategy against a database of TCR Vα and Vβ chains. A structure-based alignment ensures automated identification of CDR3 loops. The CDR are then modeled in the environment of the complex, in an ab initio approach based on a simulated annealing protocol. During this step, dihedral restraints are applied to drive the CDR1 and CDR2 loops towards their canonical conformations, described by Al-Lazikani et. al. We developed a new automated algorithm that determines additional restraints to iteratively converge towards TCR conformations making frequent hydrogen bonds with the pMHC. We demonstrated that our approach outperforms popular scoring methods (Anolea, Dope and Modeller) in predicting relevant CDR conformations. Finally, this modeling approach has been successfully applied to experimentally determined sequences of TCR that recognize the NY-ESO-1 cancer testis antigen. This analysis revealed a mechanism of selection of TCR through the presence of a single conserved amino acid in all CDR3β sequences. The important structural modifications predicted in silico and the associated dramatic loss of experimental binding affinity upon mutation of this amino acid show the good correspondence between the predicted structures and their biological activities. To our knowledge, this is the first systematic approach that was developed for large TCR repertoire structural modeling.

Spatial planning to the test of property rights in Switzerland : an innovative land management approach to coordinate spatial planning goals with property rights interests

In Switzerland, the land management regime is characterized by a liberal attitude towards the institution of property rights, which is guaranteed by the Constitution. Under the present Swiss constitutional arrangement, authorities (municipalities) are required to take into account landowners' interests when implementing their spatial planning policy. In other words, the institution of property rights cannot be restricted easily in order to implement zoning plans and planning projects. This situation causes many problems. One of them is the gap between the way land is really used by the landowners and the way land should be used based on zoning plans. In fact, zoning plans only describe how landowners should use their property. There is no sufficient provision for handling cases where the use is not in accordance with zoning plans. In particular, landowners may not be expropriated for a non-conforming use of the land. This situation often leads to the opening of new building areas in greenfields and urban sprawl, which is in contradiction with the goals set into the Federal Law on Spatial Planning. In order to identify legal strategies of intervention to solve the problem, our paper is structured into three main parts. Firstly, we make a short description of the Swiss land management regime. Then, we focus on an innovative land management approach designed to implement zoning plans in accordance with property rights. Finally, we present a case study that shows the usefulness of the presented land management approach in practice. We develop three main results. Firstly, the land management approach brings a mechanism to involve landowners in planning projects. Coordination principle between spatial planning goals and landowners' interests is the cornerstone of all the process. Secondly, the land use is improved both in terms of space and time. Finally, the institution of property rights is not challenged, since there is no expropriation and the market stays free.

Contexts and typologies in the analysis of welfare state legitimacy : a social psychological approach to political opinion formation

This dissertation analyses public opinion towards the welfare state across 29 European countries. Based on an interdisciplinary approach combining social psychological, sociological, and public opinion approaches to political opinion formation, it investigates how social position and shared beliefs shape perceived legitimacy of welfare institutions, and how social contexts impact on the processes of opinion formation. Drawing on social representations theory, as well as socialization and self-interest approaches, the dissertation analyses the role of social position in lay support for institutional solidarity. Normative beliefs-defined as preferred views regarding the organisation of social relations-mediate the effect of social position on welfare support. In addition, drawing on public opinion literature, the dissertation analyses opinion formation as a function of country-level structural (e.g., level of social spending, unemployment) and ideological factors (e.g., level of meritocracy). The dissertation comprises two theoretical and four empirical chapters. Three of the empirical chapters use data from the European Social Survey 2008. Using multilevel and typological approaches, the dissertation contributes to welfare attitude literature by showing that normative beliefs, such as distrust or egalitarianism, function as underlying mechanisms that link social position to policy attitudes (Chapter 3), and that characteristics of the national contexts influence the processes of political opinion formation (Chapters 3 and 4). Chapter 5 proposes and predicts a typology of the relationship between attitudes towards solidarity and attitudes towards control, reflecting the two central domains of government intervention. Finally, Chapter 6 examines welfare support in the realm of action and social protest, using data from a survey on Spanish Indigados activists. The findings of this dissertation inform contemporary debates about welfare state legitimacy and retrenchment. - Cette thèse avait pour but d'analyser l'opinion publique envers l'Etat social dans 29 pays européens. Basée sur une approche interdisciplinaire qui combine des perspectives psycho-sociales, sociologiques et d'opinion publique sur la formation d'opinion politique, la thèse étudie comment la position sociale et les croyances partagées façonnent la légitimité perçue des institutions de l'Etat social, et comment les contextes sociaux influencent les processus de formation d'opinion. Basée sur la théorie des représentations sociales, ainsi qu'une approche de socialisation et d'intérêt propre, cette thèse analyse le rôle des positions sociales dans le soutien envers la solidarité institutionnelle. Les croyances normatives-définies comme les visions préférées de l'organisation des rapports sociaux-médiatisent l'effet de la position sociale sur le soutien pour l'Etat social. De plus, s'inspirant de la littérature sur l'opinion publique, la thèse analyse la formation d'opinion en fonction des facteurs structurels (ex. le taux de dépenses sociales, le chômage) et idéologiques (ex. le degré de méritocratie). Cette thèse est composée de deux chapitres théoriques et quatre chapitres empiriques. Trois chapitres empiriques utilisent des données provenant de l'enquête European Social Survey 2008. Appliquant des approches multi-niveux et typoloqiques, la thèse contribue à la littérature sur les attitudes envers l'Etat social en montrant que les croyances normatives, telles que la méfiance ou l'égalitarisme, fonctionnent comme des mécanismes sous-jacents qui relient la position sociale aux attitudes politiques (Chapitre 3), et que les caractéristiques des contextes nationaux influencent les processus de formation d'opinion politique (Chapitres 3 et 4). Le chapitre 5 propose et prédit une typologie sur le rapport entre les attitudes envers la solidarité et celles envers le contrôle, renvoyant à deux domaines centraux de régulation étatique. Enfin, le chapitre 6 examine le soutien à l'Etat social dans le domaine de l'action protestataire, utilisant des données d'une enquête menée auprès des militants espagnols du mouvement des Indignés. Les résultats de cette thèse apportent des éléments qui éclairent les débats contemporains sur la légitimité de l'Etat social et son démantèlement.

Phenomenological approach to nonlinear Langevin equations

In this paper we address the problem of consistently constructing Langevin equations to describe fluctuations in nonlinear systems. Detailed balance severely restricts the choice of the random force, but we prove that this property, together with the macroscopic knowledge of the system, is not enough to determine all the properties of the random force. If the cause of the fluctuations is weakly coupled to the fluctuating variable, then the statistical properties of the random force can be completely specified. For variables odd under time reversal, microscopic reversibility and weak coupling impose symmetry relations on the variable-dependent Onsager coefficients. We then analyze the fluctuations in two cases: Brownian motion in position space and an asymmetric diode, for which the analysis based in the master equation approach is known. We find that, to the order of validity of the Langevin equation proposed here, the phenomenological theory is in agreement with the results predicted by more microscopic models

A proteomics approach to decipher the molecular nature of planarian stem cells.

Background In recent years, planaria have emerged as an important model system for research into stem cells and regeneration. Attention is focused on their unique stem cells, the neoblasts, which can differentiate into any cell type present in the adult organism. Sequencing of the Schmidtea mediterranea genome and some expressed sequence tag projects have generated extensive data on the genetic profile of these cells. However, little information is available on their protein dynamics. Results We developed a proteomic strategy to identify neoblast-specific proteins. Here we describe the method and discuss the results in comparison to the genomic high-throughput analyses carried out in planaria and to proteomic studies using other stem cell systems. We also show functional data for some of the candidate genes selected in our proteomic approach. Conclusions We have developed an accurate and reliable mass-spectra-based proteomics approach to complement previous genomic studies and to further achieve a more accurate understanding and description of the molecular and cellular processes related to the neoblasts.

A Mendelian randomization approach to assess the causal relationship of gamma-glutamyl transferase with blood pressure and insulin

Background: Elevated levels of g-glutamyl transferase (GGT) have been associated with subsequent risk of elevated blood pressure (BP), hypertension and diabetes. However, the causality of these relationships has not been addressed. Mendelian randomization refers to the random allocation of alleles at the time of gamete formation. Such allocation is expected to be independent of any behavioural and environmental factors (known or unknown), allowing the analysis of largely unconfounded risk associations that are not due to reverse causation. Methods: We performed a cross-sectional analysis among 4361 participants to the population based CoLaus study. Associations of sex-specific GGT quartiles with systolic BP, diastolic BP and insulin levels were assessed using multivariable linear regression analyses. The rs2017869 GGT1 variant, which explained 1.6% of the variance in GGT levels, was used as an instrument to perform a Mendelian randomization analysis. Results: Median age of the study population was 53 years. After age and sex adjustment, GGT quartiles were strongly associated with systolic and diastolic BP (all p for linear trend <0.0001). After multivariable adjustment, these relationships were significantly attenuated, but remained significant for systolic (b(95%CI)¼1.30 (0.32;2.03), p¼0.007) and diastolic BP (b (95%CI)¼0.57 (0.02;1.13), p¼0.04). Using Mendelian randomization, we observed no positive association of GGT with either systolic BP (b (95%CI)¼-5.68 (-11.51-0.16), p¼0.06) or diastolic BP (b (95%CI)¼ -2.24 (-5.98;1.49) p¼0.24). The association of GGT with insulin was also attenuated after multivariable adjustment. Nevertheless, a strong linear trend persisted in the fully adjusted model (b (95%CI)¼0.07 (0.04;0.09), p<0.0001). Using Mendelian randomization, we observed a similar positive association of GGT with insulin (b (95%CI)¼0.19 (0.01-0.37), p¼0.04). Conclusion: In this study, we found evidence for a direct causal relationship between GGT and insulin, suggesting that oxidative stress may be causally implicated in the pathogenesis of type 2 diabetes mellitus.

The effect of a period of intense exercise on the marker approach to detect growth hormone doping in sports.

The major objective of this study was to investigate the effects of several days of intense exercise on the growth hormone marker approach to detect doping with human growth hormone (hGH). In addition we investigated the effect of changes in plasma volume on the test. Fifteen male athletes performed a simulated nine-day cycling stage race. Blood samples were collected twice daily over a period of 15 days (stage race + three days before and after). Plasma volumes were estimated by the optimized CO Rebreathing method. IGF-1 and P-III-NP were analyzed by Siemens Immulite and Cisbio Assays, respectively. All measured GH 2000 scores were far below the published decision limits for an adverse analytical finding. The period of exercise did not increase the GH-scores; however the accompanying effect of the increase in Plasma Volume yielded in essentially lower GH-scores. We could demonstrate that a period of heavy, long-term exercise with changes in plasma volume does not interfere with the decision limits for an adverse analytical finding. Copyright © 2014 John Wiley & Sons, Ltd.

Contemporary approach to neurologic prognostication of coma after cardiac arrest.

Coma after cardiac arrest (CA) is an important cause of admission to the ICU. Prognosis of post-CA coma has significantly improved over the past decade, particularly because of aggressive postresuscitation care and the use of therapeutic targeted temperature management (TTM). TTM and sedatives used to maintain controlled cooling might delay neurologic reflexes and reduce the accuracy of clinical examination. In the early ICU phase, patients' good recovery may often be indistinguishable (based on neurologic examination alone) from patients who eventually will have a poor prognosis. Prognostication of post-CA coma, therefore, has evolved toward a multimodal approach that combines neurologic examination with EEG and evoked potentials. Blood biomarkers (eg, neuron-specific enolase [NSE] and soluble 100-β protein) are useful complements for coma prognostication; however, results vary among commercial laboratory assays, and applying one single cutoff level (eg, > 33 μg/L for NSE) for poor prognostication is not recommended. Neuroimaging, mainly diffusion MRI, is emerging as a promising tool for prognostication, but its precise role needs further study before it can be widely used. This multimodal approach might reduce false-positive rates of poor prognosis, thereby providing optimal prognostication of comatose CA survivors. The aim of this review is to summarize studies and the principal tools presently available for outcome prediction and to describe a practical approach to the multimodal prognostication of coma after CA, with a particular focus on neuromonitoring tools. We also propose an algorithm for the optimal use of such multimodal tools during the early ICU phase of post-CA coma.

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Background: MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample.Results: Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace.Conclusion: Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed.

A simple, robust and rapid approach to detect carbapenemases in Gram-negative isolates by MALDI-TOF mass spectrometry: validation with triple quadripole tandem mass spectrometry, microarray and PCR.

Carbapenemases should be accurately and rapidly detected, given their possible epidemiological spread and their impact on treatment options. Here, we developed a simple, easy and rapid matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)-based assay to detect carbapenemases and compared this innovative test with four other diagnostic approaches on 47 clinical isolates. Tandem mass spectrometry (MS-MS) was also used to determine accurately the amount of antibiotic present in the supernatant after 1 h of incubation and both MALDI-TOF and MS-MS approaches exhibited a 100% sensitivity and a 100% specificity. By comparison, molecular genetic techniques (Check-MDR Carba PCR and Check-MDR CT103 microarray) showed a 90.5% sensitivity and a 100% specificity, as two strains of Aeromonas were not detected because their chromosomal carbapenemase is not targeted by probes used in both kits. Altogether, this innovative MALDI-TOF-based approach that uses a stable 10-μg disk of ertapenem was highly efficient in detecting carbapenemase, with a sensitivity higher than that of PCR and microarray.

A general approach to the in situ energy butget of Eudendrium racemosum (Cnidaria, Hydrozoa) in the Western Mediterranean

An in situ energy budget of the hydropolyp Eudendrium racemosum (Cavolini, 1785) is presented. Ingestion and respiration rates and ammonium excretion were studied over two 24 h cycles, with two-hour sample intervals. The species ingested as much as 25.9% of its own biomass per day (minimum rate). Respiration was 1.62 ml O2 g-1 d w h-1 while excretion was 13.6 mM NH4 g-1dw h-1. We estimated that the species increased its biomass at a rate of 9.6% per day (Growth + Reproduction). This value is higher than those previously reported for other cnidarians. We can assume that the capacity of E. racemosum to survive - albeit for a limited period of the year - in the highly-competitive shallow-water communities is based on its high growth rate.

SIMSAFADIM-CLASTIC: A new approach to mathematical 3D forward simulation modelling for terrigenous and carbonate marine sedimentation

Most sedimentary modelling programs developed in recent years focus on either terrigenous or carbonate marine sedimentation. Nevertheless, only a few programs have attempted to consider mixed terrigenous-carbonate sedimentation, and most of these are two-dimensional, which is a major restriction since geological processes take place in 3D. This paper presents the basic concepts of a new 3D mathematical forward simulation model for clastic sediments, which was developed from SIMSAFADIM, a previous 3D carbonate sedimentation model. The new extended model, SIMSAFADIM-CLASTIC, simulates processes of autochthonous marine carbonate production and accumulation, together with clastic transport and sedimentation in three dimensions of both carbonate and terrigenous sediments. Other models and modelling strategies may also provide realistic and efficient tools for prediction of stratigraphic architecture and facies distribution of sedimentary deposits. However, SIMSAFADIM-CLASTIC becomes an innovative model that attempts to simulate different sediment types using a process-based approach, therefore being a useful tool for 3D prediction of stratigraphic architecture and facies distribution in sedimentary basins. This model is applied to the neogene Vallès-Penedès half-graben (western Mediterranean, NE Spain) to show the capacity of the program when applied to a realistic geologic situation involving interactions between terrigenous clastics and carbonate sediments.