Vortex-Antivortex annihilation dynamics in a square mesoscopic superconducting cylinder

The dynamics of the annihilation of a vortex-antivortex pair is investigated. The pair is activated magnetically during the run of a simulated hysteresis loop on a square mesoscopic superconducting cylinder with an antidot inserted at its center. We study the nucleation of vortices and antivortices by first increasing the magnetic field, applied parallel to the axis of the sample, from zero until the first vortex is created. A further increase of the field pulls the vortex in, until it reaches the antidot. As the polarity of the field is reversed, an antivortex enters the scene, travels toward the center of the sample and eventually the pair is annihilated. Depending on the sample size, its temperature, and Ginzburg-Landau parameter, the vortex-antivortex encounter takes place at the antidot or at the superconducting sea around it. The position and velocity of the vortex and antivortex singularities were evaluated as a function of time. The current density, magnetization and order parameter topology were also calculated.Comment: One REVTeX file and 5 EPS figure

On the weight of indels in genomic distances

Dias Vieira Braga M, Machado R, Ribeiro LC, Stoye J. On the weight of indels in genomic distances. BMC Bioinformatics. 2011;12(Suppl 9: RECOMB-CG 2011): S13.Background: Classical approaches to compute the genomic distance are usually limited to genomes with the same content, without duplicated markers. However, differences in the gene content are frequently observed and can reflect important evolutionary aspects. A few polynomial time algorithms that include genome rearrangements, insertions and deletions (or substitutions) were already proposed. These methods often allow a block of contiguous markers to be inserted, deleted or substituted at once but result in distance functions that do not respect the triangular inequality and hence do not constitute metrics. Results: In the present study we discuss the disruption of the triangular inequality in some of the available methods and give a framework to establish an efficient correction for two models recently proposed, one that includes insertions, deletions and double cut and join (DCJ) operations, and one that includes substitutions and DCJ operations. Conclusions: We show that the proposed framework establishes the triangular inequality in both distances, by summing a surcharge on indel operations and on substitutions that depends only on the number of markers affected by these operations. This correction can be applied a posteriori, without interfering with the already available formulas to compute these distances. We claim that this correction leads to distances that are biologically more plausible

Assessing logistic regression applied to respondent-driven sampling studies : a simulation study with an application to empirical data

The aim of this study is to investigate the impact of different logistic regression estimators applied to RDS studies via simulation and the analysis of empirical data. Four simulated populations were created with different connectivity characteristics. Each simulated individual received two attributes, one of them associated to the infection process. RDS samples with different sizes were obtained. The observed coverage of three logistic regression estimators were applied to assess the association between the attributes and the infection status. In simulated datasets, unweighted logistic regression estimators emerged as the best option, although all estimators showed a fairly good performance. In the empirical dataset, the performance of weighted estimators presented an unexpected behavior, making them a risky option. The unweighted logistic regression estimator is a reliable option to be applied to RDS samples, with a performance roughly similar to random samples and, therefore, should be the preferred option

\u3cem\u3eTithonia diversifolia\u3c/em\u3e for Ruminant Nutrition

India and Brazil lead the world ranking of livestock enteric methane emissions (FAO 2006). According to FAO (2006), Brazil (9.6 Tg of CH4/year) is the highest emitter of methane from cattle, followed by India (8.6 Tg of CH4/year) and the USA (5.1 Tg of CH4/year). In livestock, methane (CH4) formed from enteric fermentation of carbohydrates is primarily responsible for the emissions in the sector. Regarding livestock methane emission, Delgado et al. (2012) evaluated 20 tree and shrub species using in vitro technique and demonstrated a reducing effect on the amount of methane when Tithonia diversifolia was compared with, for example, Cynodon nlemfuensis grass. Tithonia diversifolia belongs to the division - Sphermatophyta; class - Eudicotiledoneae; sub-class - Metaclamídeas; Order - Campanulate; Family - Asteraceae; Genre - Tithonia, and Species - Tithonia diversifolia (Hemsl.), Gray (Souza 2008). Tithonia diversifolia can be very useful in animal nutrition (Fig. 1) by increasing the protein content of animal diet at low cost (Murgueitio et al. 2010) as well as in the recovery of degraded soils for it grows in areas with low levels of fertility and has high ability to absorb phosphorus, even if it is unavailable to other forage species (Kwabiah et al. 2003). The objective of this study was to assess the nutritional qualities, including quantification of enteric methane generated during in vitro ruminal fermentation, of Tithonia diversifolia as an alternative forage for ruminant nutrition in the tropics

Meningoencefalite chagásica: relato de caso de doença recentemente incluida como indicativa de AIDS no Brasil

Recently, reactivation of Chagas disease (meningoencephalitis and/or myocarditis) was included in the list of AIDS-defining illnesses in Brazil. We report a case of a 52-year-old patient with no history of previous disease who presented acute meningoencephalitis. Direct examination of blood and cerebrospinal fluid (CSF) showed Trypanosoma cruzi. CSF culture confirmed the diagnosis. Serological assays for T. cruzi and human immunodeficiency virus (HIV) were positive. Despite treatment with benznidazol and supportive measures, the patient died 24 hours after hospital admission. In endemic areas, reactivation of Chagas disease should always be considered in the differential diagnosis of meningoencephalitis among HIV-infected patients, and its presence is indicative of AIDS.Recentemente, a reagudização da doença de Chagas (meningoencefalite e/ou miocardite) foi incluída na lista de doenças indicativas de aids no Brasil. Os autores relatam o caso de um paciente de 52 anos de idade, natural de área rural da Bahia e procedente de uma área urbana de São Paulo, sem história de doenças prévias e que apresentou meningoencefalite aguda. As sorologias e pesquisas parasitológicas diretas no sangue e no liquido cefalorraquideano (LCR) demonstraram presença de Trypanosoma cruzi, confirmando-se o diagnóstico mediante cultura do LCR. O teste rápido assim como os ELISA e Western Blot diagnosticaram infecção pelo vírus da imunodeficiência humana (HIV). Apesar do tratamento com benzonidazole e as medidas de suporte, o paciente faleceu 24 horas depois da admissão hospitalar. Em áreas endêmicas, a reagudização da doença de Chagas deve ser sempre considerada no diagnóstico diferencial das meningoencefalites e sua presença em pacientes com infecção pelo HIV é indicativa de aids

Relaxation processes in harmonic glasses?

A relaxation process, with the associated phenomenology of sound attenuation and sound velocity dispersion, is found in a simulated harmonic Lennard-Jones glass. We propose to identify this process with the so called microscopic (or instantaneous) relaxation process observed in real glasses and supercooled liquids. A model based on the memory function approach accounts for the observation, and allows to relate to each others: 1) the characteristic time and strength of this process, 2) the low frequency limit of the dynamic structure factor of the glass, and 3) the high frequency sound attenuation coefficient, with its observed quadratic dependence on the momentum transfer.Comment: 11 pages, 3 figure

Saddles in the energy landscape probed by supercooled liquids

We numerically investigate the supercooled dynamics of two simple model liquids exploiting the partition of the multi-dimension configuration space in basins of attraction of the stationary points (inherent saddles) of the potential energy surface. We find that the inherent saddles order and potential energy are well defined functions of the temperature T. Moreover, decreasing T, the saddle order vanishes at the same temperature (T_MCT) where the inverse diffusivity appears to diverge as a power law. This allows a topological interpretation of T_MCT: it marks the transition from a dynamics between basins of saddles (T>T_MCT) to a dynamics between basins of minima (T<T_MCT).Comment: 4 pages, 3 figures, to be published on PR

Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi

<p>Abstract</p> <p>Background</p> <p>Lignocellulosic materials have been moved towards the forefront of the biofuel industry as a sustainable resource. However, saccharification and the production of bioproducts derived from plant cell wall biomass are complex and lengthy processes. The understanding of termite gut biology and feeding strategies may improve the current state of biomass conversion technology and bioproduct production.</p> <p>Results</p> <p>The study herein shows comprehensive functional characterization of crude body extracts from <it>Coptotermes gestroi </it>along with global proteomic analysis of the termite's digestome, targeting the identification of glycoside hydrolases and accessory proteins responsible for plant biomass conversion. The crude protein extract from <it>C. gestroi </it>was enzymatically efficient over a broad pH range on a series of natural polysaccharides, formed by glucose-, xylose-, mannan- and/or arabinose-containing polymers, linked by various types of glycosidic bonds, as well as ramification types. Our proteomic approach successfully identified a large number of relevant polypeptides in the <it>C. gestroi </it>digestome. A total of 55 different proteins were identified and classified into 29 CAZy families. Based on the total number of peptides identified, the majority of components found in the <it>C. gestroi </it>digestome were cellulose-degrading enzymes. Xylanolytic enzymes, mannan- hydrolytic enzymes, pectinases and starch-degrading and debranching enzymes were also identified. Our strategy enabled validation of liquid chromatography with tandem mass spectrometry recognized proteins, by enzymatic functional assays and by following the degradation products of specific 8-amino-1,3,6-pyrenetrisulfonic acid labeled oligosaccharides through capillary zone electrophoresis.</p> <p>Conclusions</p> <p>Here we describe the first global study on the enzymatic repertoire involved in plant polysaccharide degradation by the lower termite <it>C. gestroi</it>. The biochemical characterization of whole body termite extracts evidenced their ability to cleave all types of glycosidic bonds present in plant polysaccharides. The comprehensive proteomic analysis, revealed a complete collection of hydrolytic enzymes including cellulases (GH1, GH3, GH5, GH7, GH9 and CBM 6), hemicellulases (GH2, GH10, GH11, GH16, GH43 and CBM 27) and pectinases (GH28 and GH29).</p

Elastic constant dishomogeneity and Q2Q^2 dependence of the broadening of the dynamical structure factor in disordered systems

We propose an explanation for the quadratic dependence on the momentum $Q$, of the broadening of the acoustic excitation peak recently found in the study of the dynamic structure factor of many real and simulated glasses. We ascribe the observed $Q^2$ law to the spatial fluctuations of the local wavelength of the collective vibrational modes, in turn produced by the dishomegeneity of the inter-particle elastic constants. This explanation is analitically shown to hold for 1-dimensional disordered chains and satisfatorily numerically tested in both 1 and 3 dimensions.Comment: 4 pages, RevTeX, 5 postscript figure