Minimization of biosynthetic costs in adaptive gene expression responses of yeast to environmental changes

Yeast successfully adapts to an environmental stress by altering physiology and fine-tuning metabolism. This fine-tuning is achieved through regulation of both gene expression and protein activity, and it is shaped by various physiological requirements. Such requirements impose a sustained evolutionary pressure that ultimately selects a specific gene expression profile, generating a suitable adaptive response to each environmental change. Although some of the requirements are stress specific, it is likely that others are common to various situations. We hypothesize that an evolutionary pressure for minimizing biosynthetic costs might have left signatures in the physicochemical properties of proteins whose gene expression is fine-tuned during adaptive responses. To test this hypothesis we analyze existing yeast transcriptomic data for such responses and investigate how several properties of proteins correlate to changes in gene expression. Our results reveal signatures that are consistent with a selective pressure for economy in protein synthesis during adaptive response of yeast to various types of stress. These signatures differentiate two groups of adaptive responses with respect to how cells manage expenditure in protein biosynthesis. In one group, significant trends towards downregulation of large proteins and upregulation of small ones are observed. In the other group we find no such trends. These results are consistent with resource limitation being important in the evolution of the first group of stress responses.

Impact of open-ocean convection on particle fluxes and sediment dynamics in the deep margin of the Gulf of Lions.

Abstract. The deep outer margin of the Gulf of Lions and the adjacent basin, in the western Mediterranean Sea, are regularly impacted by open-ocean convection, a major hydrodynamic event responsible for the ventilation of the deep water in the western Mediterranean Basin. However, the impact of open-ocean convection on the flux and transport of particulate matter remains poorly understood. The variability of water mass properties (i.e., temperature and salinity), currents, and particle fluxes were monitored between September 2007 and April 2009 at five instrumented mooring lines deployed between 2050 and 2350-m depth in the deepest continental margin and adjacent basin. Four of the lines followed a NW-SE transect, while the fifth one was located on a sediment wave field to the west. The results of the main, central line SC2350 ("LION") located at 42 02.50 N, 4 410 E, at 2350-m depth, show that open-ocean convection reached midwater depth ( 1000-m depth) during winter 2007-2008, and reached the seabed ( 2350-m depth) during winter 2008-2009. Horizontal currents were unusually strong with speeds up to 39 cm s−1 during winter 2008-2009. The measurements at all 5 different locations indicate that mid-depth and near-bottom currents and particle fluxes gave relatively consistent values of similar magnitude across the study area except during winter 2008-2009, when near-bottom fluxes abruptly increased by one to two orders of magnitude. Particulate organic carbon contents, which generally vary between 3 and 5 %, were abnormally low ( 1 %) during winter 2008-2009 and approached those observed in surface sediments (0.6 %). Turbidity profiles made in the region demonstrated the existence of a bottom nepheloid layer, several hundred meters thick, and related to the resuspension of bottom sediments. These observations support the view that open-ocean deep convection events in the Gulf of Lions can cause significant remobilization of sediments in the deep outer margin and the basin, with a subsequent alteration of the seabed likely impacting the functioning of the deep-sea ecosystem.

Sensitivity of simulation results to competing SAM updates

Recently there has been a renewed research interest in the properties of non survey updates of input-output tables and social accounting matrices (SAM). Along with the venerable and well known scaling RAS method, several alternative new procedures related to entropy minimization and other metrics have been suggested, tested and used in the literature. Whether these procedures will eventually substitute or merely complement the RAS approach is still an open question without a definite answer. The performance of many of the updating procedures has been tested using some kind of proximity or closeness measure to a reference input-output table or SAM. The first goal of this paper, in contrast, is the proposal of checking the operational performance of updating mechanisms by way of comparing the simulation results that ensue from adopting alternative databases for calibration of a reference applied general equilibrium model. The second goal is to introduce a new updatin! g procedure based on information retrieval principles. This new procedure is then compared as far as performance is concerned to two well-known updating approaches: RAS and cross-entropy. The rationale for the suggested cross validation is that the driving force for having more up to date databases is to be able to conduct more current, and hopefully more credible, policy analyses.

Learning from Shocks and the Decision to Open

Two claims pervade the literature on the political economy of market reforms: that economic crises cause reforms; and that crises matter because they bring into question the validity of the economic model held to be responsible for them. Economic crises are said to spur a process of learning that is conducive to the abandonment of failing models and to the adoption of successful models. But although these claims have become the conventional wisdom, they have been hardly tested empirically due to the lack of agreement on what constitutes a crisis and to difficulties in measuring learning from them. I propose a model of rational learning from experience and apply it to the decision to open the economy. Using data from 1964 through 1990, I show that learning from the 1982 debt crisis was relevant to the first wave of adoption of an export promotion strategy, but learning was conditional on the high variability of economic outcomes in countries that opened up to trade. Learning was also symbolic in that the sheer number of other countries that liberalized was a more important driver of others’ decisions to follow suit.

On the complexity of the Whitehead minimization problem

The Whitehead minimization problem consists in finding a minimum size element in the automorphic orbit of a word, a cyclic word or a finitely generated subgroup in a finite rank free group. We give the first fully polynomial algorithm to solve this problem, that is, an algorithm that is polynomial both in the length of the input word and in the rank of the free group. Earlier algorithms had an exponential dependency in the rank of the free group. It follows that the primitivity problem – to decide whether a word is an element of some basis of the free group – and the free factor problem can also be solved in polynomial time.

Applying RADIC in Open MPI: the methodology used to implement RADIC over a Message Passing Library

Fault tolerance has become a major issue for computer and software engineers because the occurrence of faults increases the cost of using a parallel computer. RADIC is the fault tolerance architecture for message passing systems which is transparent, decentralized, flexible and scalable. This master thesis presents the methodology used to implement the RADIC architecture over Open MPI, a well-know large-used message passing library. This implementation kept the RADIC architecture characteristics. In order to validate the implementation we have executed a synthetic ping program, besides, to evaluate the implementation performance we have used the NAS Parallel Benchmarks. The results prove that the RADIC architecture performance depends on the communication pattern of the parallel application which is running. Furthermore, our implementation proves that the RADIC architecture could be implemented over an existent message passing library.

Modelling of bird distribution under complex mediterranean landscape dynamics: open habitat birds and fire (MEDFIRE)

Report for the scientific sojourn at the Simon Fraser University, Canada, from July to September 2007. General context: landscape change during the last years is having significant impacts on biodiversity in many Mediterranean areas. Land abandonment, urbanisation and specially fire are profoundly transforming large areas in the Western Mediterranean basin and we know little on how these changes influence species distribution and in particular how these species will respond to further change in a context of global change including climate. General objectives: integrate landscape and population dynamics models in a platform allowing capturing species distribution responses to landscape changes and assessing impact on species distribution of different scenarios of further change. Specific objective 1: develop a landscape dynamic model capturing fire and forest succession dynamics in Catalonia and linked to a stochastic landscape occupancy (SLOM) (or spatially explicit population, SEPM) model for the Ortolan bunting, a species strongly linked to fire related habitat in the region. Predictions from the occupancy or spatially explicit population Ortolan bunting model (SEPM) should be evaluated using data from the DINDIS database. This database tracks bird colonisation of recently burnt big areas (&50 ha). Through a number of different SEPM scenarios with different values for a number of parameter, we should be able to assess different hypothesis in factors driving bird colonisation in new burnt patches. These factors to be mainly, landscape context (i.e. difficulty to reach the patch, and potential presence of coloniser sources), dispersal constraints, type of regenerating vegetation after fire, and species characteristics (niche breadth, etc).

The Monetary policy rules and the inflation process in open emerging

This paper has three objectives. First, it aims at revealing the logic of interest rate setting pursued by monetary authorities of 12 new EU members. Using estimation of an augmented Taylor rule, we find that this setting was not always consistent with the official monetary policy. Second, we seek to shed light on the inflation process of these countries. To this end, we carry out an estimation of an open economy Philips curve (PC). Our main finding is that inflation rates were not only driven by backward persistency but also held a forward-looking component. Finally, we assess the viability of existing monetary arrangements for price stability. The analysis of the conditional inflation variance obtained from GARCH estimation of PC is used for this purpose. We conclude that inflation targeting is preferable to an exchange rate peg because it allowed decreasing the inflation rate and anchored its volatility.

Condensation of polyhedric structures onto soap films

We study the existence of solutions to general measure-minimization problems over topological classes that are stable under localized Lipschitz homotopy, including the standard Plateau problem without the need for restrictive assumptions such as orientability or even rectifiability of surfaces. In case of problems over an open and bounded domain we establish the existence of a “minimal candidate”, obtained as the limit for the local Hausdorff convergence of a minimizing sequence for which the measure is lower-semicontinuous. Although we do not give a way to control the topological constraint when taking limit yet— except for some examples of topological classes preserving local separation or for periodic two-dimensional sets — we prove that this candidate is an Almgren-minimal set. Thus, using regularity results such as Jean Taylor’s theorem, this could be a way to find solutions to the above minimization problems under a generic setup in arbitrary dimension and codimension.

Sistema de monitorització Open Source: projecte d'empresa per Computer Technology Catalunya

L’objectiu del projecte consisteix en l’estudi, simulació i implantació d’un conjunt d’aplicacions que permeten tenir un control sobre possibles problemes que puguin succeir a la nostra xarxa. Aquest projecte és la solució als problemes de detecció d’errors en el funcionament de les infraestructures de networking de les que disposen els nostres clients.

Open source framework for trucks fleet control (client)

Aquest projecte desenvolupa la part client d'una aplicació per controlar una flota de camions. Està implementada per funcionar sobre un dispositiu mòbil que funcioni amb el sistema operatiu Android.

Gestió Documental Open Source per Agresso CRM

Estudi i integració d'una aplicació Open Source especialitzada en la gestió documental amb Agresso CRM. L'objectiu d'aquesta aplicació és oferir nova funcionalitat a la gestió documental inicial i augmentar-ne les seves capacitats. Per tal de dur-lo a terme s’ha fet una recerca i un estudi d'aplicacions Open Source especialitzades en la gestió documental. Entre les aplicacions estudiades s'ha escollit KnowledgeTree pel desenvolupament de la integració, ja que era la que responia d’una manera més satisfactòria als requisits.