Genome-wide screen of genes required for caffeine tolerance in fission yeast

Background: An excess of caffeine is cytotoxic to all eukaryotic cell types. We aim to study how cells become tolerant to atoxic dose of this drug, and the relationship between caffeine and oxidative stress pathways.Methodology/Principal Findings: We searched for Schizosaccharomyces pombe mutants with inhibited growth on caffeinecontainingplates. We screened a collection of 2,700 haploid mutant cells, of which 98 were sensitive to caffeine. The genes mutated in these sensitive clones were involved in a number of cellular roles including the H2O2-induced Pap1 and Sty1 stress pathways, the integrity and calcineurin pathways, cell morphology and chromatin remodeling. We have investigated the role of the oxidative stress pathways in sensing and promoting survival to caffeine. The Pap1 and the Sty1 pathways are both required for normal tolerance to caffeine, but only the Sty1 pathway is activated by the drug. Cells lacking Pap1 aresensitive to caffeine due to the decreased expression of the efflux pump Hba2. Indeed, ?hba2 cells are sensitive to caffeine, and constitutive activation of the Pap1 pathway enhances resistance to caffeine in an Hba2-dependent manner. Conclusions/Significance: With our caffeine-sensitive, genome-wide screen of an S. pombe deletion collection, we havedemonstrated the importance of some oxidative stress pathway components on wild-type tolerance to the drug.

Prediction of enzyme function by combining sequence similarity and protein interactions

Background: A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protein sequences are more likely to perform the same function if they share similar interacting partners. Results: The method has been tested against the PSI-BLAST program using a set of 3,890 protein sequences from which interaction data was available. For protein sequences that align with at least 40% sequence identity to a known enzyme, the specificity of our method in predicting the first three EC digits increased from 80% to 90% at 80% coverage when compared to PSI-BLAST. Conclusion: Our method can also be used in proteins for which homologous sequences with known interacting partners can be detected. Thus, our method could increase 10% the specificity of genome-wide enzyme predictions based on sequence matching by PSI-BLAST alone.

Morphodynamic analysis of cerebral aneurysm pulsation from time-resolved rotational angiography

This paper presents a technique to estimate and model patient-specific pulsatility of cerebral aneurysms over onecardiac cycle, using 3D rotational X-ray angiography (3DRA) acquisitions. Aneurysm pulsation is modeled as a time varying-spline tensor field representing the deformation applied to a reference volume image, thus producing the instantaneousmorphology at each time point in the cardiac cycle. The estimated deformation is obtained by matching multiple simulated projections of the deforming volume to their corresponding original projections. A weighting scheme is introduced to account for the relevance of each original projection for the selected time point. The wide coverage of the projections, together with the weighting scheme, ensures motion consistency in all directions. The technique has been tested on digital and physical phantoms that are realistic and clinically relevant in terms of geometry, pulsation and imaging conditions. Results from digital phantomexperiments demonstrate that the proposed technique is able to recover subvoxel pulsation with an error lower than 10% of the maximum pulsation in most cases. The experiments with the physical phantom allowed demonstrating the feasibility of pulsation estimation as well as identifying different pulsation regions under clinical conditions.

Automatic low baseline stereo in urban areas

In this work we propose a new automatic methodology for computing accurate digital elevation models (DEMs) in urban environments from low baseline stereo pairs that shall be available in the future from a new kind of earth observation satellite. This setting makes both views of the scene similarly, thus avoiding occlusions and illumination changes, which are the main disadvantages of the commonly accepted large-baseline configuration. There still remain two crucial technological challenges: (i) precisely estimating DEMs with strong discontinuities and (ii) providing a statistically proven result, automatically. The first one is solved here by a piecewise affine representation that is well adapted to man-made landscapes, whereas the application of computational Gestalt theory introduces reliability and automation. In fact this theory allows us to reduce the number of parameters to be adjusted, and tocontrol the number of false detections. This leads to the selection of a suitable segmentation into affine regions (whenever possible) by a novel and completely automatic perceptual grouping method. It also allows us to discriminate e.g. vegetation-dominated regions, where such an affine model does not apply anda more classical correlation technique should be preferred. In addition we propose here an extension of the classical ”quantized” Gestalt theory to continuous measurements, thus combining its reliability with the precision of variational robust estimation and fine interpolation methods that are necessary in the low baseline case. Such an extension is very general and will be useful for many other applications as well.

Business Cycles, Unemployment Insurance, and the Calibration of Matching Models

This paper points out an empirical puzzle that arises when an RBC economy with a job matching function is used to model unemployment. The standard model can generate sufficiently large cyclical fluctuations in unemployment, or a sufficiently small response of unemployment to labor market policies, but it cannot do both. Variable search and separation, finite UI benefit duration, efficiency wages, and capital all fail to resolve this puzzle. However, both sticky wages and match-specific productivity shocks help the model reproduce the stylized facts: both make the firm's flow of surplus more procyclical, thus making hiring more procyclical too.

Implicit collusion on wide spreads

Recent empirical findings suggest that spreads quoted in dealershipmarkets might be uncompetitive. This paper analyzes theoretically if pricecompetition between risk--averse market--makers leaves room for implicitcollusive behavior. We compare the spread and risk--sharing efficiencyarising in several market structures differing in terms of i) the priorityrule followed in case of ties, and ii) the type of schedules market makersmay use, namely: general schedules, linear schedules, or limit orders. Ingeneral, competitive pricing does not arise in equilibrium, and there isa conflict between risk sharing efficiency and the tightness of the spread.This conflict can be mitigated by an appropriate market structure design.The limit order market is the only market structure in which the competitiveequilibrium is the unique equilibrium.

Turbulence and unemployment in a job matching model

According to Ljungqvist and Sargent (1998), high European unemployment since the 1980s can be explained by a rise in economic turbulence, leading to greater numbers of unemployed workers with obsolete skills. These workers refuse new jobs due to high unemployment benefits. In this paper we reassess the turbulence-unemployment relationship using a matching model with endogenous job destruction. In our model, higher turbulence reduces the incentives of employed workers to leave their jobs. If turbulence has only a tiny effect on the skills of workers experiencing endogenous separation, then the results of Lungqvist and Sargent (1998, 2004) are reversed, and higher turbulence leads to a reduction in unemployment. Thus, changes in turbulence cannot provide an explanation for European unemployment that reconciles the incentives of both unemployed and employed workers.

General preferences for consumption goods in the random matching model of commodity money

This paper generalizes the original random matching model of money byKiyotaki and Wright (1989) (KW) in two aspects: first, the economy ischaracterized by an arbitrary distribution of agents who specialize in producing aparticular consumption good; and second, these agents have preferences suchthat they want to consume any good with some probability. The resultsdepend crucially on the size of the fraction of producers of each goodand the probability with which different agents want to consume eachgood. KW and other related models are shown to be parameterizations ofthis more general one.

How wide is the gap? An investigation of gender wage differences using quantile regression

In this paper we examine the determinants of wages and decompose theobserved differences across genders into the "explained by differentcharacteristics" and "explained by different returns components"using a sample of Spanish workers. Apart from the conditionalexpectation of wages, we estimate the conditional quantile functionsfor men and women and find that both the absolute wage gap and thepart attributed to different returns at each of the quantiles, farfrom being well represented by their counterparts at the mean, aregreater as we move up in the wage range.

Informational matching

This paper analyzes the problem of matching heterogeneous agents in aBayesian learning model. One agent gives a noisy signal to another agent,who is responsible for learning. If production has a strong informationalcomponent, a phase of cross-matching occurs, so that agents of low knowledgecatch up with those of higher one. It is shown that:(i) a greater informational component in production makes cross-matchingmore likely;(ii) as the new technology is mastered, production becomes relatively morephysical and less informational;(iii) a greater dispersion of the ability to learn and transfer informationmakes self-matching more likely; and(iv) self-matching leads to more self-matching, whereas cross-matching canmake less productive agents overtake more productive ones.

Shocks and institutions in a job matching model

This paper explains the divergent behavior of European an US unemploymentrates using a job market matching model of the labor market with aninteraction between shocks an institutions. It shows that a reduction inTF growth rates, an increase in real interest rates, and an increase intax rates leads to a permanent increase in unemployment rates when thereplacement rates or initial tax rates are high, while no increase inunemployment occurs when institutions are "employment friendly". The paperalso shows that an increase in turbulence, modelle as an increase probabilityof skill loss, is not a robust explanation for the European unemploymentpuzzle in the context of a matching model with both endogenous job creationand job estruction.

Business cycles, unemployment insurance and the calibration of matching models

This paper theoretically and empirically documents a puzzle that arises when an RBC economy with a job matching function is used to model unemployment. The standard model can generate sufficiently large cyclical fluctuations in unemployment, or a sufficiently small response of unemployment to labor market policies, but it cannot do both. Variable search and separation, finite UI benefit duration, efficiency wages, and capital all fail to resolve this puzzle. However, either sticky wages or match-specific productivity shocks can improve the model's performance by making the firm's flow of surplus more procyclical, which makes hiring more procyclical too.

Endogeneous matching in university-industry collaboration: Theory and empirical evidence from the UK

We develop a two-sided matching model to analyze collaboration between heterogeneousacademics and firms. We predict a positive assortative matching in terms of both scientificability and affinity for type of research, but negative assortative in terms of ability on one sideand affinity in the other. In addition, the most able and most applied academics and the mostable and most basic firms shall collaborate rather than stay independent. Our predictionsreceive strong support from the analysis of the teams of academics and firms that proposeresearch projects to the UK's Engineering and Physical Sciences Research Council.

MSISpIC: A Probabilistic Scan Matching Algorithm Using a Mechanical Scanned Imaging Sonar

This paper compares two well known scan matching algorithms: the MbICP and the pIC. As a result of the study, it is proposed the MSISpIC, a probabilistic scan matching algorithm for the localization of an Autonomous Underwater Vehicle (AUV). The technique uses range scans gathered with a Mechanical Scanning Imaging Sonar (MSIS), and the robot displacement estimated through dead-reckoning with the help of a Doppler Velocity Log (DVL) and a Motion Reference Unit (MRU). The proposed method is an extension of the pIC algorithm. Its major contribution consists in: 1) using an EKF to estimate the local path traveled by the robot while grabbing the scan as well as its uncertainty and 2) proposing a method to group into a unique scan, with a convenient uncertainty model, all the data grabbed along the path described by the robot. The algorithm has been tested on an AUV guided along a 600m path within a marina environment with satisfactory results