Pareto Optimal Matchings in Many-to-Many Markets with Ties

We consider Pareto-optimal matchings (POMs) in a many-to-many market of applicants and courses where applicants have preferences, which may include ties, over individual courses and lexicographic preferences over sets of courses. Since this is the most general setting examined so far in the literature, our work unifies and generalizes several known results. Specifically, we characterize POMs and introduce the \emph{Generalized Serial Dictatorship Mechanism with Ties (GSDT)} that effectively handles ties via properties of network flows. We show that GSDT can generate all POMs using different priority orderings over the applicants, but it satisfies truthfulness only for certain such orderings. This shortcoming is not specific to our mechanism; we show that any mechanism generating all POMs in our setting is prone to strategic manipulation. This is in contrast to the one-to-one case (with or without ties), for which truthful mechanisms generating all POMs do exist

A simple scheme for allocating capital in a foreign exchange proprietary trading firm

We present a model of capital allocation in a foreign exchange proprietary trading firm. The owner allocates capital to individual traders, who operate within strict risk limits. Traders specialize in individual currencies, but are given discretion over their choice of trading rule. The owner provides the simple formula that determines position sizes – a formula that does not require estimation of the firm-level covariance matrix. We provide supporting empirical evidence of excess risk-adjusted returns to the firm-level portfolio, and we discuss a modification of the model in which the owner dictates the choice of trading rule

A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments

The volatile compound dimethylsulphide (DMS) is important in climate regulation, the sulphur cycle and signalling to higher organisms. Microbial catabolism of the marine osmolyte dimethylsulphoniopropionate (DMSP) is thought to be the major biological process generating DMS. Here we report the discovery and characterisation of the first gene for DMSP-independent DMS production in any bacterium. This gene, mddA, encodes a methyltransferase that methylates methanethiol (MeSH) and generates DMS. MddA functions in many taxonomically diverse bacteria including sediment-dwelling pseudomonads, nitrogen-fixing bradyrhizobia and cyanobacteria, and mycobacteria, including the pathogen Mycobacterium tuberculosis. The mddA gene is present in metagenomes from varied environments, being particularly abundant in soil environments, where it is predicted to occur in up to 76% of bacteria. This novel pathway may significantly contribute to global DMS emissions, especially in terrestrial environments, and could represent a shift from the notion that DMSP is the only significant precursor of DMS

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery1,2, spreading efficiently via low-dose fecal-oral transmission3,4. Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality4-6. Classical approaches have shown S. sonnei is genetically conserved and clonal7. We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage

Enabling comparative modeling of closely related genomes: Example genus Brucella

For many scientific applications, it is highly desirable to be able to compare metabolic models of closely related genomes. In this short report, we attempt to raise awareness to the fact that taking annotated genomes from public repositories and using them for metabolic model reconstructions is far from being trivial due to annotation inconsistencies. We are proposing a protocol for comparative analysis of metabolic models on closely related genomes, using fifteen strains of genus Brucella, which contains pathogens of both humans and livestock. This study lead to the identification and subsequent correction of inconsistent annotations in the SEED database, as well as the identification of 31 biochemical reactions that are common to Brucella, which are not originally identified by automated metabolic reconstructions. We are currently implementing this protocol for improving automated annotations within the SEED database and these improvements have been propagated into PATRIC, Model-SEED, KBase and RAST. This method is an enabling step for the future creation of consistent annotation systems and high-quality model reconstructions that will support in predicting accurate phenotypes such as pathogenicity, media requirements or type of respiration.We thank Jean Jacques Letesson, Maite Iriarte, Stephan Kohler and David O'Callaghan for their input on improving specific annotations. This project has been funded by the United States National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract No. HHSN272200900040C, awarded to BW Sobral, and from the United States National Science Foundation under Grant MCB-1153357, awarded to CS Henry. J.P.F. acknowledges funding from [FRH/BD/70824/2010] of the FCT (Portuguese Foundation for Science and Technology) Ph.D. scholarship

Bacterial microevolution and the Pangenome

The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history

Simulation of natural convective boundary layer flow of a nanofluid past a convectively heated inclined plate in the presence of magnetic field

AbstractThis paper deals with the numerical simulation of transient magnetohydrodynamics natural convective boundary layer flow of a nanofluid over an inclined plate. In the modeling of nanofluids, dynamic effects including the Brownian motion and thermophoresis are taken into account. Numerical solutions have been computed via the Galerkin-finite element method. The effects of angle of inclination, buoyancy-ratio parameter, Brownian motion, thermophoresis and magnetic field are taken into account and controlled by non-dimensional parameters. To compute the rate of convergence and error of the computed numerical solution, the double mesh principle is used. Similarity solutions are calculated and presented graphically for non-dimensional velocity, temperature, local rate of heat and mass transfer with pertinent parameters. The modified Nusselt number decreases with increasing inclination angle, buoyancy-ratio parameter, Brownian motion and thermophoresis parameter, whereas it increases with increasing Prandtl number. Validation of the results is achieved with earlier results for forced convective flow and non-magnetic studies. Such problems have several applications in engineering and petroleum industries such as electroplating, chemical processing of heavy metals and solar water heaters. External magnetic fields play an important role in electrical power generation, inclination/acceleration sensors, fine-tuning of the final materials to industrial specification because of their controlling behaviour on the flow characteristics of nanofluids