Vortex ratchet reversal: The role of interstitial vortices

Triangular arrays of Ni nanotriangles embedded in superconducting Nb films exhibit unexpected dynamical vortex effects. Collective pinning with a vortex lattice configuration different from the expected fundamental triangular "Abrikosov state" is found. The vortex motion which prevails against the triangular periodic potential is produced by channelling effects between triangles. Interstitial vortices coexisting with pinned vortices in this asymmetric potential, lead to ratchet reversal, i.e. a DC output voltage which changes sign with the amplitude of an applied alternating drive current. In this landscape, ratchet reversal is always observed at all magnetic fields (all numbers of vortices) and at different temperatures. The ratchet reversal is unambiguously connected to the presence of two locations for the vortices: interstitial and above the artificial pinning sites.Comment: 21 pages, 4 figures, 1 Tabl

Bioinformatic approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection

The objective of the present study was to compare genetic and phenotypic variation of 103 Saccharomyces cerevisiae strains isolated from winemaking environments. We used bioinformatics approaches to identify genetically similary strains with specific phenotypes and to estimate a strain's biotechnological potential. 
A S. cerevisiae collection, comprising 440 strains that were obtained from winemaking environments in Portugal has been constituted during the last years. All strains were genetically characterized by a set of eleven highly polymorphic microsatellites and showed unique allelic combinations. Using neural networks, a subset of 103 genetically most diverse strains was chosen for phenotypic analysis, that included growth in synthetic must media at various temperatures, utilization of carbon sources (glucose, ribose, arabinose, xylose, saccharose, galactose, rafinose, maltose, glycerol, potassium acetate and pyruvic acid), growth in ethanol containing media, evaluation of osmotic and oxidative stress resistance, H2S production and utilization of different nitrogen sources. Using supervised data mining approaches we have found that genotype represented with presence/absence of eleven microsatellites relates well with geographical location (performance evaluation using leave-out-out technique resulted in high performance scores; e.g., area under ROC curve was above 0.8 for a number of standard machine learning approaches tested). To find relations between phenotypes and genotypes, we used a two-step approach which first hierarchically clusters the strains according to their phenotype, and then tests if the resulting sub-clusters are identifiable using strain’s genetic data. Several groups of strains with similar phenotype profiles and common features in genotype were identified this way, and they are subject to further investigations. 

Financially supported by the programs POCI 2010 (FEDER/FCT, POCTI/AGR/56102/2004) and AGRO (ENOSAFE, Nº 762).
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The warm and dense Galaxy - tracing the formation of dense cloud structures out to the Galactic Center

The past two decades have seen extensive surveys of the far-infrared to submillimeter continuum emission in the plane of our Galaxy. We line out prospects for the coming decade for corresponding molecular and atomic line surveys which are needed to fully understand the formation of the dense structures that give birth to clusters and stars out of the diffuse interstellar medium. We propose to work towards Galaxy wide surveys in mid-J CO lines to trace shocks from colliding clouds, Galaxy-wide surveys for atomic Carbon lines in order to get a detailed understanding of the relation of atomic and molecular gas in clouds, and to perform extensive surveys of the structure of the dense parts of molecular clouds to understand the importance of filaments/fibers over the full range of Galactic environments and to study how dense cloud cores are formed from the filaments. This work will require a large (50m) Single Dish submillimeter telescope equipped with massively multipixel spectrometer arrays, such as envisaged by the AtLAST project.Comment: Science white paper submitted to the Astro2020 Decadal Surve

Computational models reveal genotype-phenotype associations in Saccharomyces cerevisiae

Genome sequencing is essential to understand individual variation and to study the mechanisms that explain relations between genotype and phenotype. The accumulated knowledge from large-scale genome sequencing projects of Saccharomyces cerevisiae isolates is being used to study the mechanisms that explain such relations. Our objective was to undertake genetic characterization of 172 S. cerevisiae strains from different geographical origins and technological groups, using 11 polymorphic microsatellites, and computationally relate these data with the results of 30 phenotypic tests. Genetic characterization revealed 280 alleles, with the microsatellite ScAAT1 contributing most to intrastrain variability, together with alleles 20, 9 and 16 from the microsatellites ScAAT4, ScAAT5 and ScAAT6. These microsatellite allelic profiles are characteristic for both the phenotype and origin of yeast strains. We confirm the strength of these associations by construction and cross-validation of computational models that can predict the technological application and origin of a strain from the microsatellite allelic profile. Associations between microsatellites and specific phenotypes were scored using information gain ratios, and significant findings were confirmed by permutation tests and estimation of false discovery rates. The phenotypes associated with higher number of alleles were the capacity to resist to sulphur dioxide (tested by the capacity to grow in the presence of potassium bisulphite) and the presence of galactosidase activity. Our study demonstrates the utility of computational modelling to estimate a strain technological group and phenotype from microsatellite allelic combinations as tools for preliminary yeast strain selection. Copyright (C) 2014 John Wiley & Sons, Ltd.Ricardo Franco-Duarte and Ines Mendes are the recipients of fellowships from the Portuguese Science Foundation (FCT; Grant Nos SFRH/BD/74798/2010 and SFRH/BD/48591/2008, respectively) and Joao Drumonde-Neves is the recipient of a fellowship from the Azores Government (Grant No. M3.1.2/F/006/2008; DRCT). Financial support was obtained from FEDER funds through the programme COMPETE and by national funds through FCT by Project Nos FCOMP-01-0124-008775 (PTDC/AGR-ALI/103392/2008) and PTDC/AGR-ALI/121062/2010. Lan Umek and Blaz Zupan acknowledge financial support from the Slovene Research Agency (Grant No. P2-0209). The authors would like also to thank all the researchers who kindly provided yeast strains: Gianni Liti, Institute of Genetics, UK; Laura Carreto, CESAM and Biology Department, Portugal; Goto Yamamoto, NRIB, Japan; Cletus Kurtzman, Microbial Properties Research, USA; Rogelio Brandao, Laboratorio de Fisologia e Bioquimica de Microorganismos, Brazil; and Huseyin Erten, Cukurova University, Turkey.info:eu-repo/semantics/publishedVersio

The geographic distribution of saccharomyces cerevisiae isolates within three Italian neighboring winemaking regions reveals strong differences in yeast abundance, genetic diversity and industrial strain dissemination

In recent years the interest for natural fermentations has been re-evaluated in terms of increasing the wine terroir and managing more sustainable winemaking practices. Therefore, the level of yeast genetic variability and the abundance of Saccharomyces cerevisiae native populations in vineyard are becoming more and more crucial at both ecological and technological level. Among the factors that can influence the strain diversity, the commercial starter release that accidentally occur in the environment around the winery, has to be considered. In this study we led a wide scale investigation of S. cerevisiae genetic diversity and population structure in the vineyards of three neighboring winemaking regions of Protected Appellation of Origin, in North-East of Italy. Combining mtDNA RFLP and microsatellite markers analyses we evaluated 634 grape samples collected over 3 years. We could detect major differences in the presence of S. cerevisiae yeasts, according to the winemaking region. The population structures revealed specificities of yeast microbiota at vineyard scale, with a relative Appellation of Origin area homogeneity, and transition zones suggesting a geographic differentiation. Surprisingly, we found a widespread industrial yeast dissemination that was very high in the areas where the native yeast abundance was low. Although geographical distance is a key element involved in strain distribution, the high presence of industrial strains in vineyard reduced the differences between populations. This finding indicates that industrial yeast diffusion it is a real emergency and their presence strongly interferes with the natural yeast microbiota

Resonant Raman scattering off neutral quantum dots

Resonant inelastic (Raman) light scattering off neutral GaAs quantum dots which contain a mean number, N=42, of electron-hole pairs is computed. We find Raman amplitudes corresponding to strongly collective final states (charge-density excitations) of similar magnitude as the amplitudes related to weakly collective or single-particle excitations. As a function of the incident laser frequency or the magnetic field, they are rapidly varying amplitudes. It is argued that strong Raman peaks should come out in the spin-density channels, not related to valence-band mixing effects in the intermediate states.Comment: Accepted in Physical Review

Survey of molecular methods for the typing of wine yeast strains

A survey of the genetic polymorphisms produced by distinct methods was performed in 23 commercial winery yeast strains. The microsatellite typing, using 6 different loci, an optimized interdelta sequence analysis and RFLP of mitochondrial DNA generated by the enzyme Hinf I had the same discriminatory power: among the 23 commercial yeast strains, 21 distinct patterns were obtained. Karyotype analysis originated 22 patterns, thereby allowing the discrimination of one of the three strains that were not distinguished by the other methods. Due to the equivalence of the results obtained in this survey, any of the methods can be applied at the industrial scale.Fundação para a Ciência e a Tecnologia (FCT) - POCTI/BIO/38106/2001 (Eixo 2, Medida 2.3, QCAIII - FEDER).Instituto de Cooperação Científica e Tecnológica Internacional (ICCTI) - grant nº 657 C2.Comunidade Europeia (UE) - contract number QLK4-CT-2001-51873

Rocking ratchet induced by pure magnetic potentials with broken reflection symmetry

A ratchet effect (the rectification of an ac injected current) which is purely magnetic in origin has been observed in a superconducting-magnetic nanostructure hybrid. The hybrid consists of a superconducting Nb film in contact with an array of nanoscale magnetic triangles, circular rings or elliptical rings. The arrays were placed into well-defined remanent magnetic states by application of different magnetic field cycles. The stray fields from these remanent states provide a magnetic landscape which influences the motion of superconducting vortices. We examined both randomly varying landscapes from demagnetized samples, and ordered landscapes from samples at remanence after saturation in which the magnetic rings form parallel onion states containing two domain walls. The ratchet effect is absent if the rings are in the demagnetized state or if the vortices propagate parallel to the magnetic reflection symmetry axis (perpendicular to the magnetic domain walls) in the ordered onion state. On the other hand, when the vortices move perpendicular to the magnetic reflection symmetry axis in the ordered onion state (parallel to the domain walls) a clear ratchet effect is observed. This behavior differs qualitatively from that observed in samples containing arrays of triangular Ni nanostructures, which show a ratchet of structural origin.Comment: 16 pages, 6 figures and 1 tabl

The auditory cortex of the bat Phyllostomus discolor: Localization and organization of basic response properties

<p>Abstract</p> <p>Background</p> <p>The mammalian auditory cortex can be subdivided into various fields characterized by neurophysiological and neuroarchitectural properties and by connections with different nuclei of the thalamus. Besides the primary auditory cortex, echolocating bats have cortical fields for the processing of temporal and spectral features of the echolocation pulses. This paper reports on location, neuroarchitecture and basic functional organization of the auditory cortex of the microchiropteran bat <it>Phyllostomus discolor </it>(family: Phyllostomidae).</p> <p>Results</p> <p>The auditory cortical area of <it>P. discolor </it>is located at parieto-temporal portions of the neocortex. It covers a rostro-caudal range of about 4800 μm and a medio-lateral distance of about 7000 μm on the flattened cortical surface.</p> <p>The auditory cortices of ten adult <it>P. discolor </it>were electrophysiologically mapped in detail. Responses of 849 units (single neurons and neuronal clusters up to three neurons) to pure tone stimulation were recorded extracellularly. Cortical units were characterized and classified depending on their response properties such as best frequency, auditory threshold, first spike latency, response duration, width and shape of the frequency response area and binaural interactions.</p> <p>Based on neurophysiological and neuroanatomical criteria, the auditory cortex of <it>P. discolor </it>could be subdivided into anterior and posterior ventral fields and anterior and posterior dorsal fields. The representation of response properties within the different auditory cortical fields was analyzed in detail. The two ventral fields were distinguished by their tonotopic organization with opposing frequency gradients. The dorsal cortical fields were not tonotopically organized but contained neurons that were responsive to high frequencies only.</p> <p>Conclusion</p> <p>The auditory cortex of <it>P. discolor </it>resembles the auditory cortex of other phyllostomid bats in size and basic functional organization. The tonotopically organized posterior ventral field might represent the primary auditory cortex and the tonotopically organized anterior ventral field seems to be similar to the anterior auditory field of other mammals. As most energy of the echolocation pulse of <it>P. discolor </it>is contained in the high-frequency range, the non-tonotopically organized high-frequency dorsal region seems to be particularly important for echolocation.</p

UM ESTUDO EXPLORATÓRIO SOBRE O USO DE SOFTWARES EM PESQUISAS QUALITATIVAS: UM APARTE NO ÂMBITO DA EDUCAÇÃO FÍSICA

Este trabalho trata-se de uma pesquisa bibliográfica com objetivo de verificar a frequência da utilização de softwares de pesquisa qualitativa, ademais conferir como o uso dos softwares mais frequentes foram empregados ao longo dos últimos anos e ainda verificar a utilização deles na área da Educação Física. Realizou-se uma busca no Portal de Periódicos da Capes, de artigos publicados entre 2005 a 2015, acerca da utilização dos termos WebQDA, Atlas.ti, MaxQDA e Nvivo. Encontrou-se 2056 publicações que empregaram termos referentes a estes softwares, entre estas, o termo mais constante na literatura foi o Nvivo, o qual apareceu em um total de 1476 publicações. Ao verificar a utilização do termo mais citado na área de “Educação Física”, encontrou-se 16 trabalhos. Observou-se um crescimento na utilização desses recursos tecnológicos em pesquisas qualitativas ao longo dos últimos anos, apesar deles ainda serem pouco empregados, inclusive na área da Educação Física