Removing zero Lyapunov exponents in volume-preserving flows

Baraviera and Bonatti proved that it is possible to perturb, in the c^1 topology, a volume-preserving and partial hyperbolic diffeomorphism in order to obtain a non-zero sum of all the Lyapunov exponents in the central direction. In this article we obtain the analogous result for volume-preserving flows.Comment: 10 page

The silicon stable isotope distribution along the GEOVIDE section (GEOTRACES GA-01) of the North Atlantic Ocean

The stable isotope composition of dissolved silicon in seawater (δ30SiDSi) was examined at 10 stations along the GEOVIDE section (GEOTRACES GA-01), spanning the North Atlantic Ocean (40–60∘ N) and Labrador Sea. Variations in δ30SiDSi below 500 m were closely tied to the distribution of water masses. Higher δ30SiDSi values are associated with intermediate and deep water masses of northern Atlantic or Arctic Ocean origin, whilst lower δ30SiDSi values are associated with DSi-rich waters sourced ultimately from the Southern Ocean. Correspondingly, the lowest δ30SiDSi values were observed in the deep and abyssal eastern North Atlantic, where dense southern-sourced waters dominate. The extent to which the spreading of water masses influences the δ30SiDSi distribution is marked clearly by Labrador Sea Water (LSW), whose high δ30SiDSi signature is visible not only within its region of formation within the Labrador and Irminger seas, but also throughout the mid-depth western and eastern North Atlantic Ocean. Both δ30SiDSi and hydrographic parameters document the circulation of LSW into the eastern North Atlantic, where it overlies southern-sourced Lower Deep Water. The GEOVIDE δ30SiDSi distribution thus provides a clear view of the direct interaction between subpolar/polar water masses of northern and southern origin, and allow examination of the extent to which these far-field signals influence the local δ30SiDSi distribution

Re-annotation of the genome sequence of Helicobacter pylori 26695

Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastriculcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.This work was supported by the project FCOMP-01-0124-FEDER-009707, entitled HeliSysBio molecular Systems Biology in Helicobacter pylori (Ref.: FCT PTDC/EBB-EBI/104235/2008). Daniela Correia is grateful for financial support from the FCT (PhD grant: SFRH/BD/47596/2008)

Black string corrections in variable tension braneworld scenarios

Braneworld models with variable tension are investigated, and the corrections on the black string horizon along the extra dimension are provided. Such corrections are encrypted in additional terms involving the covariant derivatives of the variable tension on the brane, providing profound consequences concerning the black string horizon variation along the extra dimension, near the brane. The black string horizon behavior is shown to be drastically modified by the terms corrected by the brane variable tension. In particular, a model motivated by the phenomenological interesting case regarding Eotvos branes is investigated. It forthwith provides further physical features regarding variable tension braneworld scenarios, heretofore concealed in all previous analysis in the literature. All precedent analysis considered uniquely the expansion of the metric up to the second order along the extra dimension, what is able to evince solely the brane variable tension absolute value. Notwithstanding, the expansion terms aftermath, further accomplished in this paper from the third order on, elicits the successive covariant derivatives of the brane variable tension, and their respective coupling with the extrinsic curvature, the Weyl tensor, and the Riemann and Ricci tensors, as well as the scalar curvature. Such additional terms are shown to provide sudden modifications in the black string horizon in a variable tension braneworld scenarioComment: 12 pages, 5 figures, accepted in PR

Notes on the Two-brane Model with Variable Tension

Motivated by possible extensions of the braneworld models with two branes, we investigate some consequences of a variable brane tension using the well established results on consistency conditions. By a slight modification of the usual stress-tensor used in order to derive the braneworld sum rules, we find out some important constraints obeyed by time dependent brane tensions. In particular it is shown that the tensions of two Randall-Sundrum like branes obeying, at the same time, an Eotvos law, aggravate the fine tuning problem. Also, it is shown that if the hidden brane tension obeys an Eotvos law, then the visible brane has a mixed behavior allowing a bouncing-like period at early times while it is dominated by an Eotvos law nowadays. To finalize, we discuss some qualitative characteristics which may arise in the scope of dynamical brane tensions, as anisotropic background and branons production.Comment: 7 pages, 1 figure, accepted for publication in Physical Review

Health-Related Quality of Life in Portuguese Patients with Chronic Hepatitis C

INTRODUCTION: Chronic hepatitis C virus (HCV) infection impacts multiple health and psychosocial dimensions and encompasses a significant overall burden as it progresses to advanced stages of hepatic disease. AIMS: To evaluate for the first time health-related quality of life (HRQoL) of a subset of Portuguese adult patients with chronic hepatitis C using the Portuguese versions of generic, Short-Form 12 Health Survey (SF-12v2), and disease-specific, Chronic Liver Disease Questionnaire (CLDQ), instruments; to assess psychometric properties of CLDQ, Portuguese version. METHODS: HRQoL was evaluated in Portuguese adult outpatients with chronic hepatitis C attending the Hepatology Clinic at Centro Hospitalar do Porto, using SF-12v2 and CLDQ. This transversal study was conducted between April and October 2015. RESULTS: Eighty outpatients with chronic hepatitis C were enrolled, with mean age 57 years (standard deviation 11), 67.5% male, all Caucasian, 76.3% diagnosed for >10 years, 66.3% with C virus genotype 1, 65.0% with hepatic cirrhosis (94.2% of which Child-Pugh A), and 46.3% under current antiviral treatment. For CLDQ internal consistency, Cronbach's α was 0.88; for construct validity, correlations ranged from 0.36 to 0.80 (p < 0.01). Mean CLDQ scores ranged from 4.25 (Worry) to 5.78 (Abdominal Symptoms). Lower scores were observed for Worry, Fatigue, and Emotional Function domains. Statistically significant differences were found in median values of Worry (CLDQ) and Role Emotional (SF-12) (p < 0.05) for "current antiviral treatment," with higher scores for patients that concluded therapy. CONCLUSION: HRQoL was negatively affected in several domains in Portuguese patients with chronic hepatitis C; oral antiviral treatment correlated with better quality of life, assuring its benefits on this population; the CLDQ Portuguese version revealed adequate psychometric properties, and was useful in assessing quality of life in Portuguese HCV patients.info:eu-repo/semantics/publishedVersio

Flexible and user friendly tools for the incorporation of fluxomics data into metabolic models

The measurement of fluxes and the understanding of their control are at the core of Metabolic Engineering (ME). In this context, this work presents two integrated open- source software tools that allow to perform tasks of metabolic flux analysis (MFA). Both are platform independent, written in Java, and interact with the OptFlux framework [1], which also facilitates their communication (Figure 1). OptFlux is a modular open-source software that incorporates tools for strain optimization, i.e., the identification of ME targets. It also provides tools to use stoichiometric metabolic models for phenotype simulation of both wild-type and mutant organisms, using methods such as the well known Flux Balance Analysis (FBA). Graphical user interfaces are made available for every operation and to check the results that are obtained. Moreover, a network visualization system is offered, where simulation results can be added to overlap the network graph. The developed tools exploit OptFluxâ??s capabilities in terms of model interaction, simulation methods and visualization features. The first proposed software, named MetabolIc NEtwork Ratio AnaLysis (MiNeRAl) (Figure 1, bottom), aims at analyzing labeling experiments to infer flux constraints that for stoichiometric models. From a set of measurements of a 13C-labelling experiment, mass isotopomer distribution vectors (MDV) are calculated. If aminoacids are measured, the measured fragments, coupled with a carbon transition map provided by the user, are used to determine their precursors, and the corresponding MDVs are calculated. Based on the set of MDVs, the software uses the carbon transitions to determine the flux ratios that produce a given metabolite through the different pathways. These ratios are probabilistic equations that translate how the 13C-labeling pattern is distributed throughout the metabolic network [2]. Since the calculation of the flux ratios is independent of the flux distribution, this software can be used independently of other flux calculation processes, and the ratios can be further exploited to reduce the degrees of freedom of systems obtained in other MFA approaches [3,4]. The main differentiating characteristics of this tool are, besides being usr-friendly, the fact that it is generic for any type of metabolite fragmentation originating from GC-MS techniques and metabolic network topology. Furthermore, the software is also able to investigate what flux ratio constraints are possible to be inferred for a certain experiment beforehand. On the other hand, the second software application here described, jMFA (Figure 1, top), is focused on using different types of experimental flux data to constrain metabolic models and improve their predictions with a variety of tools. It allows users to define constraints associated with measured fluxes and/ or flux ratios, together with environmental conditions (e.g. media) and reaction/ gene knockouts. The application identifies the set of applicable methods based on the constraints defined from user inputs, allowing to select the desired approach, encompassing algebraic and constraint- based simulation methods (such as Flux Balance Analysis and its variants). Anytime a set of constraints is selected, the software calculates the degrees of freedom of the configured system, and updates the admissible methods depending on whether the system is underdetermined, determined or overdetermined, as shown in Figure 1. A method to perform robustness analysis is also implemented. The integration of jMFA within the OptFlux framework allows the use of different model formats and the integration with complementary methods for phenotype simulation and visualization of the results. Moreover, the flux ratio constraints can be obtained from previous calculations in MiNeRAl, or manually defined by the user. The first option provides a straightforward way to integrate both applications in a ME workflow

Assignment of novel functions to Helicobacter pylori 26695’s genome and reconstruction of a genome-scale metabolic model

Helicobacter pylori is a pathogenic organism associated with human gastric diseases. The development of mathematical models of metabolism is now considered a fundamental part of the study of the cell. For the particular case of microorganisms associated with human diseases, information on metabolic and regulatory networks can be used to understand the molecular factors of the microorganism that are likely to interact with the host and cause diseases. The availability of the genome sequence of H. pylori 26695 and its annotation has allowed in the past the construction of a metabolic model for this organism. The first genome-scale metabolic model for H. pylori 26695 was published in 2002 (iCS291) and a corrected reconstruction was published in 2005 (iIT341 GSM/GPR). The main goal of the present work was to update H. pylori’s genome-scale metabolic model based on the new information made available. For that purposes, using new annotation methodologies and data available in databases, an assignment of novel functions to H. pylori 26695’s genome was performed. For a total of 510 “hypothetical proteins” (almost 1/3 of the genes) identified in the last re-annotation, 137 new functions were attributed. A total of 581 E.C. numbers were assigned to CDS, being 528 complete E.C. numbers. This new information was used as the basis of the model reconstruction. In addition, transport reactions in the model were updated. The biomass equation was reviewed and H. pylori biomass coefficients and composition were adjusted. The obtained model successfully predicted the nutritional requirements and amino acids essentialities, which were experimentally validated. As a result, the present work presents a new H. pylori 26695 genome-scale metabolic model with more accurate and reliable predictions and can be used to identify potential targets for designing more effective drugs for H. pylori inactivation

Assignment of novel functions to Helicobacter pylori 26695’s genome

Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers as well as gastric cancer. The genome of H. pylori 26695 has been sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695’s genes was performed. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated E.C. numbers to metabolic genes, and the assignment of 177 new functions to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.(undefined