Long-Lived Non-Equilibrium Interstitial-Solid-Solutions in Binary Mixtures

We perform particle resolved experimental studies on the heterogeneous crystallisation process of two compo- nent mixtures of hard spheres. The components have a size ratio of 0.39. We compared these with molecular dynamics simulations of homogenous nucleation. We find for both experiments and simulations that the final assemblies are interstitial solid solutions, where the large particles form crystalline close-packed lattices, whereas the small particles occupy random interstitial sites. This interstitial solution resembles that found at equilibrium when the size ratios are 0.3 [Filion et al., Phys. Rev. Lett. 107, 168302 (2011)] and 0.4 [Filion, PhD Thesis, Utrecht University (2011)]. However, unlike these previous studies, for our system sim- ulations showed that the small particles are trapped in the octahedral holes of the ordered structure formed by the large particles, leading to long-lived non-equilibrium structures in the time scales studied and not the equilibrium interstitial solutions found earlier. Interestingly, the percentage of small particles in the crystal formed by the large ones rapidly reaches a maximum of around 14% for most of the packing fractions tested, unlike previous predictions where the occupancy of the interstitial sites increases with the system concentration. Finally, no further hopping of the small particles was observed

MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: Unraveling the sulfur cycle

The increasing number of metagenomic and genomic sequences has dramatically improved our understanding of microbial diversity, yet our ability to infer metabolic capabilities in such datasets remains challenging. We describe the Multigenomic Entropy Based Score pipeline (MEBS), a software platform designed to evaluate, compare, and infer complex metabolic pathways in large "omic" datasets, including entire biogeochemical cycles. MEBS is open source and available through https://github.com/eead-csic-compbio/metagenome Pfam score. To demonstrate its use, we modeled the sulfur cycle by exhaustively curating the molecular and ecological elements involved (compounds, genes, metabolic pathways, and microbial taxa). This information was reduced to a collection of 112 characteristic Pfam protein domains and a list of complete-sequenced sulfur genomes. Using the mathematical framework of relative entropy (H''), we quantitatively measured the enrichment of these domains among sulfur genomes. The entropy of each domain was used both to build up a final score that indicates whether a (meta)genomic sample contains the metabolic machinery of interest and to propose marker domains in metagenomic sequences such as DsrC (PF04358). MEBS was benchmarked with a dataset of 2107 non-redundant microbial genomes from RefSeq and 935 metagenomes from MG-RAST. Its performance, reproducibility, and robustness were evaluated using several approaches, including random sampling, linear regression models, receiver operator characteristic plots, and the area under the curve metric (AUC). Our results support the broad applicability of this algorithm to accurately classify (AUC = 0.985) hard-to-culture genomes (e.g., Candidatus Desulforudis audaxviator), previously characterized ones, and metagenomic environments such as hydrothermal vents, or deep-sea sediment. Our benchmark indicates that an entropy-based score can capture the metabolic machinery of interest and can be used to efficiently classify large genomic and metagenomic datasets, including uncultivated/unexplored taxa

The Holstein Polaron

We describe a variational method to solve the Holstein model for an electron coupled to dynamical, quantum phonons on an infinite lattice. The variational space can be systematically expanded to achieve high accuracy with modest computational resources (12-digit accuracy for the 1d polaron energy at intermediate coupling). We compute ground and low-lying excited state properties of the model at continuous values of the wavevector $k$ in essentially all parameter regimes. Our results for the polaron energy band, effective mass and correlation functions compare favorably with those of other numerical techniques including DMRG, Global Local and exact diagonalization. We find a phase transition for the first excited state between a bound and unbound system of a polaron and an additional phonon excitation. The phase transition is also treated in strong coupling perturbation theory.Comment: 24 pages, 11 figures submitted to PR

The importance of lizards and small mammals as reservoirs for Borrelia lusitaniae in Portugal

Borrelia lusitaniae is a pathogen frequent in the Mediterranean area. Apart from lizards, evidence for birds and small mammals as competent reservoirs for this genospecies has been occasional. We collected questing ticks, skin biopsies and Ixodes sp. ticks feeding on lizards, birds and small mammals in a B. burgdorferi s.l. enzootic area to assess their importance in the maintenance of B. lusitaniae. B. lusitaniae was the most prevalent genospecies in questing ticks and was commonly found in larvae feeding on Psammodromus algirus. One biopsy infected with B. lusitaniae was collected from the tail of one Podarcis hispanica, which suggests systemic infection. I. ricinus larvae feeding on Apodemus sylvaticus were infected with B. lusitaniae but with a lower prevalence. Our results reinforce the importance of lizards as reservoirs for B. lusitaniae, suggesting that P. algirus, in particular, acts as main reservoir for B. lusitaniae in Portugal

Quantitative plane-resolved crystal growth and dissolution kinetics by coupling in situ optical microscopy and diffusion models : the case of salicylic acid in aqueous solution

The growth and dissolution kinetics of salicylic acid crystals are investigated in situ by focusing on individual microscale crystals. From a combination of optical microscopy and finite element method (FEM) modeling, it was possible to obtain a detailed quantitative picture of dissolution and growth dynamics for individual crystal faces. The approach uses real-time in situ growth and dissolution data (crystal size and shape as a function of time) to parametrize a FEM model incorporating surface kinetics and bulk to surface diffusion, from which concentration distributions and fluxes are obtained directly. It was found that the (001) face showed strong mass transport (diffusion) controlled behavior with an average surface concentration close to the solubility value during growth and dissolution over a wide range of bulk saturation levels. The (1̅10) and (110) faces exhibited mixed mass transport/surface controlled behavior, but with a strong diffusive component. As crystals became relatively large, they tended to exhibit peculiar hollow structures in the end (001) face, observed by interferometry and optical microscopy. Such features have been reported in a number of crystals, but there has not been a satisfactory explanation for their origin. The mass transport simulations indicate that there is a large difference in flux across the crystal surface, with high values at the edge of the (001) face compared to the center, and this flux has to be redistributed across the (001) surface. As the crystal grows, the redistribution process evidently can not be maintained so that the edges grow at the expense of the center, ultimately creating high index internal structures. At later times, we postulate that these high energy faces, starved of material from solution, dissolve and the extra flux of salicylic acid causes the voids to close

Perceived feasibility of computer-generated auralization in concert halls

Over the years auralization has become a useful tool for simulating and evaluating the listening experience in virtual environments. Psychoacoustic phenomena, embodied by the human hearing system, highly determine the accuracy of sound-field recreation that is required for seemingly feasible auralization. In this scenario, the main aim of this study is to assess the suitability of computer-generated room impulse responses when used for auralizing spaces. To this purpose, simulated and experimentally measured binaural room impulse responses (BRIRs) have been convolved with iconic musical excerpts for various representative seats within a medium-sized concert hall. Listening tests have been thereby conducted and their results will be shown, analyzed and discussedEn estos últimos años, la auralización se ha convertido en una herramienta útil para la simulación y evaluación de la experiencia del oyente en entornos virtuales. En este ámbito, son de especial importancia los aspectos psicológicos y perceptivos, derivados del funcionamiento del sistema auditivo y del cerebro humanos, que determinan la precisión que se requiere para una recreación aparentemente creíble del campo sonoro. En este contexto, el principal objetivo de este estudio es evaluar la validez de respuestas al impulso de la sala generadas por ordenador para su utilización en la auralización de espacios. Con este propósito, para algunas localidades representativas de una sala de conciertos de tamaño medio, se han convolucionado varias respuestas al impulso binaurales (BRIRs), simuladas y medidas experimentalmente, con fragmentos musicales conocidos. Con los datos obtenidos, se han llevado a cabo pruebas de audición, cuyos resultados se presentan, analizan y discuten en esta comunicació

Adverse childhood experiences and suicide attempts in morbidly obese adults

Introdução: As tentativas de suicídio surgem frequentemente associadas a problemas alimentares, tanto anorexia quanto bulimia. Do mesmo modo, tem-se verifi cado uma elevada ocorrência de suicídio entre obesos. Investigações têm mostrado que a adversidade na infância pode ser um fator de risco para as tentativas de suicídio. Objetivos: Caracterizar e compreender a relação entre experiências de adversidade na infância e tentativas de suicídio em 100 obesos mórbidos candidatos a cirurgia bariátrica. Métodos: Um total de 100 pacientes foram selecionados de setembro de 2007 a outubro de 2007 e de janeiro de 2008 a janeiro de 2009, sendo que 20 pacientes eram do sexo feminino. A média de idade era de 38,89±9,87 anos, e a média do peso máximo era de 136,43±14 kg. O Questionário da História de Adversidade na Infância foi utilizado para avaliar experiências adversas. Resultados: 88% dos pacientes relataram a existência de pelo menos uma experiência de adversidade na infância, e 25% relataram já ter realizado pelo menos uma tentativa de suicídio. A adversidade na infância esteve associada a um risco aumentado para realizar tentativas de suicídio (odds ratio = 2,026). Conclusão: Esses dados devem ser levados em consideração na avaliação e no acompanhamento desses pacientes.Introduction: Suicide attempts are often associated with eating disorders, both anorexia and bulimia. Likewise, a high incidence of suicide has been observed among obese patients. Previous studies have shown that adverse experiences in childhood may be a risk factor for suicide attempts. Objectives: To characterize and to understand the relationship between adverse experiences and suicide attempts in 100 morbidly obese patients referred for bariatric surgery. Methods: A total of 100 patients were selected from September 2007 to October 2007 and from January 2008 to January 2009. Of these, 20 patients were females. Mean age was 38.89±9.87 years, and mean maximum weight was 136.43±14 kg. The Portuguese version of the Family ACE (Adverse Childhood Experiences) Questionnaire was used to assess the occurrence of adverse events. Results: 88% of the patients reported the existence of at least one adverse experience in childhood, and 25% reported at least one previous suicide attempt. Adversity in childhood was associated with an increased risk for suicide attempts (odds ratio = 2.026). Conclusion: These data should be taken into account in the assessment and monitoring of these patients.Fundação para a Ciência e a Tecnologia (FCT); (SFRH/BD/37069/2007)