Spectral Analysis for Matrix Hamiltonian Operators

In this work, we study the spectral properties of matrix Hamiltonians generated by linearizing the nonlinear Schr\"odinger equation about soliton solutions. By a numerically assisted proof, we show that there are no embedded eigenvalues for the three dimensional cubic equation. Though we focus on a proof of the 3d cubic problem, this work presents a new algorithm for verifying certain spectral properties needed to study soliton stability. Source code for verification of our comptuations, and for further experimentation, are available at http://www.math.toronto.edu/simpson/files/spec_prop_code.tgz.Comment: 57 pages, 22 figures, typos fixe

Developing tools for Mycosphaerella fijiensis studies.

Mycosphaerella fijiensis is the causal agent of the black leaf streak disease, or Black Sigatoka, the most devasting fungal disease of banana around the world.Edição do Fast Firward 40 jaar Gewasbescherming, 2009, Wageningen

101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species

Impact of Donor Milk on Short- and Long-Term Growth of Very Low Birth Weight Infants

Mother’s own milk (MOM) reduces the risk of morbidities in very low birth weight (VLBW) infants. When MOM is unavailable, donor breastmilk (DM) is used, with unclear impact on short- and long-term growth. This retrospective analysis compared anthropometric data at six time points from birth to 20–24 months corrected age in VLBW infants who received MOM supplements of preterm formula (n = 160) versus fortified DM (n = 161) during neonatal intensive care unit (NICU) hospitalization. The cohort was 46% female; mean birth weight and gestational age (GA) were 998 g and 27.3 weeks. Multilevel linear growth models assessed changes in growth z-scores short-term (to NICU discharge) and long-term (post-discharge), controlling for amount of DM or formula received in first 28 days of life, NICU length of stay (LOS), birth GA, and sex. Z-scores for weight and length decreased during hospitalization but increased for all parameters including head circumference post-discharge. Short-term growth was positively associated with LOS and birth GA. A higher preterm formula proportion, but not DM proportion, was associated with slower rates of decline in short-term growth trajectories, but feeding type was unrelated to long-term growth. In conclusion, controlling for total human milk fed, DM did not affect short- or long-term growth

Generation of transgenic Mycosphaerella fijiensis expressing reporter genes: tools for pathogenicity and mating studies.

Mycosphaerella fijiensis, the causal agent of black leaf streak disease is the most devastating pathogen of banana and plantains. Detailed studies on the plant pathogen interaction as well as mating behavior could be improved by the use of non-destructive reporter gene assays. M. fijiensis isolates from different global populations and opposite mating types, CIRAD86 (Mat1-1) from Cameroon and CIRAD139A (Mat1-2) from Colombia, were selected for our studies. In order to generate transgenic M. fijiensis strains, two gene constructs carrying either reporter genes gfp (green fluorescent protein) or dsred (Discosoma sp. red fluorescent protein) driven by the constitutive promoter PtoxA were used. Both constructs also carried the hph gene for resistance to the antibiotic hygromycin as selective marker. Transformation procedures mediated by Agrobacterium tumefaciens strain LBA1100 were carried out using macerated mycelium from 3-week-old cultures of CIRAD86 and CIRAD139A. After the cocultivation period, the cultures were transferred to selective medium containing 30 mg/l hygromycin. Transgenic events were identified by fluorescent microscopy observations after 2-3 weeks. In this part of the work, we were able to generate transgenic strains from both isolates expressing either reporter genes, namely CIRAD86::GFP, CIRAD86::DsRed, CIRAD139A::GFP and CIRAD139A::DsRed. Simultaneously, pathogenicity validation screens and mating assays using in vitro leaf fragments are also being conducted in order to characterize the different stages in the pathogenesis on banana

Weak Sequential Composition in Process Algebras

n this paper we study a special operator for sequential composition, which is defined relative to a dependency relation over the actions of a given system. The idea is that actions which are not dependent (intuitively because they share no common resources) do not have to wait for one another to proceed, even if they are composed sequentially. Such a notion has been studied before in a linear-time setting, but until recently there has been no systematic investigation in the context of process algebras. We give a structural operational semantics for a process algebraic language containing such a sequential composition operator, which shows some interesting interplay with choice. We give a complete axiomatisation of strong bisimilarity and we show consistency of the operational semantics with an event-based denotational semantics developed recently by the second author. The axiom system allows to derive the communication closed layers law, which in the linear time setting has been shown to be a very useful instrument in correctness preserving transformations. We conclude with a couple of examples

Air temperature changes in Toruń (central Poland) from 1871 to 2010

The article presents a detailed analysis of changes in air temperature in Toruń in the period 1871–2010 on the basis of homogenised monthly, seasonal and annual air temperature series which have been newly constructed (i.e. extended by the 50 years of 1871–1920). Over the 140-year study period, a sizeable and statistically significant increase of 0.1 °C per decade was found in the air temperature in Toruń. The greatest increases occurred for spring and winter, at 0.12 and 0.11 °C, respectively. A lesser warming, meanwhile, was recorded for autumn (0.10 °C/10 years), and particularly for summer (0.07 °C/10 years). The air temperature trends are statistically significant for all seasons. Air temperature differences between the monthly averages of three analysed subperiods (1871–1900, 1901–1950 and 1951–2010) and averages for the entire period under review rarely exceeded ± 0.5 °C. In all of these periods, the highest average air temperatures occurred in July and the lowest in January. The period of 1981–2010 had the highest frequency of occurrence of very and extremely warm seasons and years. Meanwhile, the highest frequency of very and extremely cool seasons and years was recorded in the 1940s and in the nineteenth century. In the period of 1871–2010, winters shortened markedly (by 7%) and summers lengthened by 3.8%. All of the presented aspects of air temperature in Toruń, which is representative of the climate of central Poland, are in close agreement with the findings of analogous studies of the same for other areas of Poland and Central Europe

Finished genome of the fungal wheat pathogen Mycosphaerella graminicola Reveals dispensome structure, chromosome plasticity, and stealth pathogenesis.

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Preference for biological motion is reduced in ASD: implications for clinical trials and the search for biomarkers

Background: The neurocognitive mechanisms underlying autism spectrum disorder (ASD) remain unclear. Progress has been largely hampered by small sample sizes, variable age ranges and resulting inconsistent findings. There is a pressing need for large definitive studies to delineate the nature and extent of key case/control differences to direct research towards fruitful areas for future investigation. Here we focus on perception of biological motion, a promising index of social brain function which may be altered in ASD. In a large sample ranging from childhood to adulthood, we assess whether biological motion preference differs in ASD compared to neurotypical participants (NT), how differences are modulated by age and sex and whether they are associated with dimensional variation in concurrent or later symptomatology. Methods: Eye-tracking data were collected from 486 6-to-30-year-old autistic (N = 282) and non-autistic control (N = 204) participants whilst they viewed 28 trials pairing biological (BM) and control (non-biological, CTRL) motion. Preference for the biological motion stimulus was calculated as (1) proportion looking time difference (BM-CTRL) and (2) peak look duration difference (BM-CTRL). Results: The ASD group showed a present but weaker preference for biological motion than the NT group. The nature of the control stimulus modulated preference for biological motion in both groups. Biological motion preference did not vary with age, gender, or concurrent or prospective social communicative skill within the ASD group, although a lack of clear preference for either stimulus was associated with higher social-communicative symptoms at baseline. Limitations: The paired visual preference we used may underestimate preference for a stimulus in younger and lower IQ individuals. Our ASD group had a lower average IQ by approximately seven points. 18% of our sample was not analysed for various technical and behavioural reasons. Conclusions: Biological motion preference elicits small-to-medium-sized case–control effects, but individual differences do not strongly relate to core social autism associated symptomatology. We interpret this as an autistic difference (as opposed to a deficit) likely manifest in social brain regions. The extent to which this is an innate difference present from birth and central to the autistic phenotype, or the consequence of a life lived with ASD, is unclear