Mapping the Space of Genomic Signatures

We propose a computational method to measure and visualize interrelationships among any number of DNA sequences allowing, for example, the examination of hundreds or thousands of complete mitochondrial genomes. An "image distance" is computed for each pair of graphical representations of DNA sequences, and the distances are visualized as a Molecular Distance Map: Each point on the map represents a DNA sequence, and the spatial proximity between any two points reflects the degree of structural similarity between the corresponding sequences. The graphical representation of DNA sequences utilized, Chaos Game Representation (CGR), is genome- and species-specific and can thus act as a genomic signature. Consequently, Molecular Distance Maps could inform species identification, taxonomic classifications and, to a certain extent, evolutionary history. The image distance employed, Structural Dissimilarity Index (DSSIM), implicitly compares the occurrences of oligomers of length up to $k$ (herein $k=9$) in DNA sequences. We computed DSSIM distances for more than 5 million pairs of complete mitochondrial genomes, and used Multi-Dimensional Scaling (MDS) to obtain Molecular Distance Maps that visually display the sequence relatedness in various subsets, at different taxonomic levels. This general-purpose method does not require DNA sequence homology and can thus be used to compare similar or vastly different DNA sequences, genomic or computer-generated, of the same or different lengths. We illustrate potential uses of this approach by applying it to several taxonomic subsets: phylum Vertebrata, (super)kingdom Protista, classes Amphibia-Insecta-Mammalia, class Amphibia, and order Primates. This analysis of an extensive dataset confirms that the oligomer composition of full mtDNA sequences can be a source of taxonomic information.Comment: 14 pages, 7 figures. arXiv admin note: substantial text overlap with arXiv:1307.375

Tactical allocation in commodity futures markets: Combining momentum and term structure signals

This paper examines the combined role of momentum and term structure signals for the design of profitable trading strategies in commodity futures markets. With significant annualized alphas of 10.14% and 12.66%, respectively, the momentum and term structure strategies appear profitable when implemented individually. With an abnormal return of 21.02%, our double-sort strategy that exploits both momentum and term structure signals clearly outperforms the single-sort strategies. This double-sort strategy can additionally be utilized as a portfolio diversification tool. The abnormal performance of the combined portfolios cannot be explained by a lack of liquidity, data mining or transaction costs

A System Dynamics Model to Identify the Impact of the Economic Crisis on Crime Rate and on Security Sensation in European Societies

Modern society is a Complicated System, in which the interaction between its essential parts is affected in a daily basis by: (a) the Economic Crisis, (b) the Feeling of Xenophobia, (c) the Interweaving of the Political System and (d) the Degeneration of Human Interpersonal Relationships. Two important facts that have been excessively observed in the European Union over the last few years are the increase of Crime Rate, and at the same time the decrease of Security Sensation. The model that we have developed simulates the way that particular social phenomena such as: (a) the taxation, (b) the reduction of the State Expenditure on Equipment and (c) the conflicts of interest caused by the Economic Crisis, affect the Crime Rate. Therefore, this study can be the starting point for identifying other social phenomena that should be taken into account in the Strategic Plan of Crime and Violence treatment in member countries of the European Union

Incorporating real time velocity map image reconstruction into closed-loop coherent control

We report techniques developed to utilize three-dimensional momentum information as feedback in adaptive femtosecond control of molecular dynamics. Velocity map imaging is used to obtain the three-dimensional momentum map of the dissociating ions following interaction with a shaped intense ultrafast laser pulse. In order to recover robust feedback information, however, the two-dimensional momentum projection from the detector must be inverted to reconstruct the full three-dimensional momentum of the photofragments. These methods are typically slow or require manual inputs and are therefore accomplished offline after the images have been obtained. Using an algorithm based upon an “onion-peeling” (also known as “back projection”) method, we are able to invert 1040 × 1054 pixel images in under 1 s. This rapid inversion allows the full photofragment momentum to be used as feedback in a closed-loop adaptive control scheme, in which a genetic algorithm tailors an ultrafast laser pulse to optimize a specific outcome. Examples of three-dimensional velocity map image based control applied to strong-field dissociation of CO and O2 are presented

Influence of Branching on the Rheology, Filmability and Mechanical and Optical Properties of a Biodegradable and Compostable Co-Polyester

Over the last years, bio-based and biodegradable alternatives have gained considerable attention both of academic and of packaging industrial communities, driven by recent legislation and increasing awareness concerning environmental issues related to traditional plastic. However, it is often observed that packaging products made from bioplastics do not exhibit comparable performance to those produced using common non-biodegradable ones. The presence of long chain branching improves the processing behavior under elongational flow and, then, the filmability of low viscosity polymers such as polyesters. In this work it has been demonstrated that the presence of long chain branching in a bio-co-polyester, induced by the use of pentaerythritol in the synthesis a of poly(butylene adipate-co-butylene terephthalate), is able to dramatically change the rheological behavior of the linear chain polyester improving its filmability. The addition of branching lead to an increase of the elastic modulus and the tensile strength in branched polyester films if compared to the linear ones, while the elongation at break decreased. This is due to the answer of the branched polyester to the non-isothermal elongational flow that allows a better orientation of the macromolecules of the branched polyester. The film obtained with the branched polyester showed a decrease in clarity and a slight increase in haze if compared to linear one due to differences in the morphology of the two samples

The longevity and reversibility of quiescence in Schizosaccharomyces pombe are dependent upon the HIRA histone chaperone

Quiescence (G0) is a reversible non-dividing state that facilitates cellular survival in adverse conditions. Here, we demonstrate that the HIRA histone chaperone complex is required for the reversibility and longevity of nitrogen starvation-induced quiescence in Schizosaccharomyces pombe. The HIRA protein, Hip1 is not required for entry into G0 or the induction of autophagy. Although hip1Δ cells retain metabolic activity in G0, they rapidly lose the ability to resume proliferation. After a short period in G0 (1 day), hip1Δ mutants can resume cell growth in response to the restoration of a nitrogen source but do not efficiently reenter the vegetative cell cycle. This correlates with a failure to induce the expression of MBF transcription factor-dependent genes that are critical for S phase. In addition, hip1Δ G0 cells rapidly progress to a senescent state in which they can no longer re-initiate growth following nitrogen source restoration. Analysis of a conditional hip1 allele is consistent with these findings and indicates that HIRA is required for efficient exit from quiescence and prevents an irreversible cell cycle arrest