Formal Context Generation using Dirichlet Distributions

We suggest an improved way to randomly generate formal contexts based on Dirichlet distributions. For this purpose we investigate the predominant way to generate formal contexts, a coin-tossing model, recapitulate some of its shortcomings and examine its stochastic model. Building up on this we propose our Dirichlet model and develop an algorithm employing this idea. By comparing our generation model to a coin-tossing model we show that our approach is a significant improvement with respect to the variety of contexts generated. Finally, we outline a possible application in null model generation for formal contexts.Comment: 16 pages, 7 figure

A Memetic Analysis of a Phrase by Beethoven: Calvinian Perspectives on Similarity and Lexicon-Abstraction

This article discusses some general issues arising from the study of similarity in music, both human-conducted and computer-aided, and then progresses to a consideration of similarity relationships between patterns in a phrase by Beethoven, from the first movement of the Piano Sonata in A flat major op. 110 (1821), and various potential memetic precursors. This analysis is followed by a consideration of how the kinds of similarity identified in the Beethoven phrase might be understood in psychological/conceptual and then neurobiological terms, the latter by means of William Calvin’s Hexagonal Cloning Theory. This theory offers a mechanism for the operation of David Cope’s concept of the lexicon, conceived here as a museme allele-class. I conclude by attempting to correlate and map the various spaces within which memetic replication occurs

Multi-level selectional stalemate in a simple artificial chemistry

We describe a simple artificial chemistry which abstracts a small number of key features from the origin of life "replicator world" hypotheses. We report how this can already give rise to moderately complex and counter-intuitive evolutionary phenomena, including macro- evolutionary deterioration in replication fidelity (which corresponds to intrinsic replicator fitness in this model). We briefly describe the extension of this model to incorporate a higher, protocell, level of selection. We show that the interaction between the two levels of selection then serves to control parasitic exploitation at the molecular level, while still significantly constraining accessible evolutionary trajectories at the protocell level. We conclude with a brief discussion of the implications for further work

Introduction to protein folding for physicists

The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the conformational behaviour of flexible molecules is nothing more than a complex physical problem, increasingly more physicists are moving into the study of protein systems, bringing with them powerful mathematical and computational tools, as well as the sharp intuition and deep images inherent to the physics discipline. This work attempts to facilitate the first steps of such a transition. In order to achieve this goal, we provide an exhaustive account of the reasons underlying the protein folding problem enormous relevance and summarize the present-day status of the methods aimed to solving it. We also provide an introduction to the particular structure of these biological heteropolymers, and we physically define the problem stating the assumptions behind this (commonly implicit) definition. Finally, we review the 'special flavor' of statistical mechanics that is typically used to study the astronomically large phase spaces of macromolecules. Throughout the whole work, much material that is found scattered in the literature has been put together here to improve comprehension and to serve as a handy reference.Comment: 53 pages, 18 figures, the figures are at a low resolution due to arXiv restrictions, for high-res figures, go to http://www.pabloechenique.co

Evolutionary instability of Zero Determinant strategies demonstrates that winning isn't everything

Zero Determinant (ZD) strategies are a new class of probabilistic and conditional strategies that are able to unilaterally set the expected payoff of an opponent in iterated plays of the Prisoner's Dilemma irrespective of the opponent's strategy, or else to set the ratio between a ZD player's and their opponent's expected payoff. Here we show that while ZD strategies are weakly dominant, they are not evolutionarily stable and will instead evolve into less coercive strategies. We show that ZD strategies with an informational advantage over other players that allows them to recognize other ZD strategies can be evolutionarily stable (and able to exploit other players). However, such an advantage is bound to be short-lived as opposing strategies evolve to counteract the recognition.Comment: 14 pages, 4 figures. Change in title (again!) to comply with Nature Communications requirements. To appear in Nature Communication

Paclitaxel-Eluting Coronary Stents in Patients With Diabetes Mellitus Pooled Analysis From 5 Randomized Trials

ObjectivesWe sought to examine the safety and efficacy of paclitaxel-eluting stents (PES) in patients with diabetes mellitus (DM).BackgroundCompared with patients without DM, patients with DM undergoing percutaneous coronary intervention are at increased risk for mortality and restenosis. The safety of drug-eluting stents in diabetic patients has recently been called into question by a published meta-analysis of randomized trials.MethodsPatient-level data were pooled from 5 prospective, double-blind, randomized trials of PES versus bare-metal stents (BMS) (n = 3,513). Safety and efficacy outcomes through 4 years of follow-up were assessed among the 827 randomized patients (23.6%) with DM.ResultsPatients treated with PES and BMS has similar baseline characteristics among both the diabetic and nondiabetic cohorts within these trials. At 4-year follow-up, there were no significant differences between PES and BMS among diabetic patients in the rates of death (8.4% vs. 10.3%, respectively, p = 0.61), myocardial infarction (6.9% vs. 8.9%, p = 0.17), or stent thrombosis (1.4% vs. 1.2%, p = 0.92). Treatment of diabetic patients with PES compared with treatment with BMS was associated with a significant and durable reduction in target lesion revascularization over the 4-year follow-up period (12.4% vs. 24.7%, p < 0.0001). The relative safety and efficacy of PES compared with the relative safety and efficacy of BMS in diabetic patients extended to both those requiring and not requiring insulin.ConclusionsIn these 5 randomized trials in which patients with single, primarily noncomplex lesions were enrolled, treatment with PES compared with treatment with BMS was safe and effective, resulting in markedly lower rates of target lesion revascularization at 4 years, with similar rates of death, myocardial infarction, and stent thrombosis

High-Efficiency Resonant RF Spin Rotator with Broad Phase Space Acceptance for Pulsed Polarized Cold Neutron Beams

We have developed a radio-frequency resonant spin rotator to reverse the neutron polarization in a 9.5 cm x 9.5 cm pulsed cold neutron beam with high efficiency over a broad cold neutron energy range. The effect of the spin reversal by the rotator on the neutron beam phase space is compared qualitatively to RF neutron spin flippers based on adiabatic fast passage. The spin rotator does not change the kinetic energy of the neutrons and leaves the neutron beam phase space unchanged to high precision. We discuss the design of the spin rotator and describe two types of transmission-based neutron spin-flip efficiency measurements where the neutron beam was both polarized and analyzed by optically-polarized 3He neutron spin filters. The efficiency of the spin rotator was measured to be 98.0+/-0.8% on resonance for neutron energies from 3.3 to 18.4 meV over the full phase space of the beam. As an example of the application of this device to an experiment we describe the integration of the RF spin rotator into an apparatus to search for the small parity-violating asymmetry A_gamma in polarized cold neutron capture on para-hydrogen by the NPDGamma collaboration at LANSCE

‘O sibling, where art thou?’ – a review of avian sibling recognition with respect to the mammalian literature

Avian literature on sibling recognition is rare compared to that developed by mammalian researchers. We compare avian and mammalian research on sibling recognition to identify why avian work is rare, how approaches differ and what avian and mammalian researchers can learn from each other. Three factors: (1) biological differences between birds and mammals, (2) conceptual biases and (3) practical constraints, appear to influence our current understanding. Avian research focuses on colonial species because sibling recognition is considered adaptive where ‘mixing potential’ of dependent young is high; research on a wider range of species, breeding systems and ecological conditions is now needed. Studies of acoustic recognition cues dominate avian literature; other types of cues (e.g. visual, olfactory) deserve further attention. The effect of gender on avian sibling recognition has yet to be investigated; mammalian work shows that gender can have important influences. Most importantly, many researchers assume that birds recognise siblings through ‘direct familiarisation’ (commonly known as associative learning or familiarity); future experiments should also incorporate tests for ‘indirect familiarisation’ (commonly known as phenotype matching). If direct familiarisation proves crucial, avian research should investigate how periods of separation influence sibling discrimination. Mammalian researchers typically interpret sibling recognition in broad functional terms (nepotism, optimal outbreeding); some avian researchers more successfully identify specific and testable adaptive explanations, with greater relevance to natural contexts. We end by reporting exciting discoveries from recent studies of avian sibling recognition that inspire further interest in this topic

The Atmospheric Coupling and Dynamics Across the Mesopause (ACaDAMe) mission

The Atmospheric Coupling and Dynamics Across the Mesopause (ACaDAMe) is a mission designed to uniquely address critical questions involving multi-scale wave dynamics at key space weather (SWx) “gateway altitudes” of the mesosphere and lower thermosphere (MLT) at ∼70–150 km. ACaDAMe observes with a nadir-pointing resonant lidar that utilizes the fluorescence of atomic Na present in the MLT. By tuning a laser to the Na absorption wavelength (589 nm), ACaDAMe would perform very high resolution measurements of temperature and Na densities across the mesopause during both day and night. In this manner, Na is used as tracer for observing and characterizing MLT waves generated by tropospheric weather that represent the dominant terrestrial source of energy and momentum affecting space weather and transport of mesospheric species