The semi-classical expansion and resurgence in gauge theories: new perturbative, instanton, bion, and renormalon effects

We study the dynamics of four dimensional gauge theories with adjoint fermions for all gauge groups, both in perturbation theory and non-perturbatively, by using circle compactification with periodic boundary conditions for the fermions. There are new gauge phenomena. We show that, to all orders in perturbation theory, many gauge groups are Higgsed by the gauge holonomy around the circle to a product of both abelian and nonabelian gauge group factors. Non-perturbatively there are monopole-instantons with fermion zero modes and two types of monopole-anti-monopole molecules, called bions. One type are "magnetic bions" which carry net magnetic charge and induce a mass gap for gauge fluctuations. Another type are "neutral bions" which are magnetically neutral, and their understanding requires a generalization of multi-instanton techniques in quantum mechanics - which we refer to as the Bogomolny-Zinn-Justin (BZJ) prescription - to compactified field theory. The BZJ prescription applied to bion-anti-bion topological molecules predicts a singularity on the positive real axis of the Borel plane (i.e., a divergence from summing large orders in peturbation theory) which is of order N times closer to the origin than the leading 4-d BPST instanton-anti-instanton singularity, where N is the rank of the gauge group. The position of the bion--anti-bion singularity is thus qualitatively similar to that of the 4-d IR renormalon singularity, and we conjecture that they are continuously related as the compactification radius is changed. By making use of transseries and Ecalle's resurgence theory we argue that a non-perturbative continuum definition of a class of field theories which admit semi-classical expansions may be possible.Comment: 112 pages, 7 figures; v2: typos corrected, discussion of supersymmetric models added at the end of section 8.1, reference adde

Evaluation and Validation of a Real-Time PCR Assay for Detection and Quantitation of Human Adenovirus 14 from Clinical Samples

In 2007, the Centers for Disease Control and Prevention (CDC) reported that Human adenovirus type 14 (HAdV-14) infected 106 military personnel and was responsible for the death of one U.S. soldier at Lackland Air Force Base in Texas. Identification of the responsible adenovirus, which had not previously been seen in North America and for which rapid diagnostic tools were unavailable, required retrospective analysis at reference laboratories. Initial quarantine measures were also reliant on relatively slow traditional PCR analysis at other locations. To address this problem, we developed a real-time PCR assay that detects a 225 base pair sequence in the HAdV-14a hexon gene. Fifty-one oropharyngeal swab specimens from the Naval Health Research Center, San Diego, CA and Advanced Diagnostic Laboratory, Lackland AFB, TX were used to validate the new assay. The described assay detected eight of eight and 19 of 19 confirmed HAdV-14a clinical isolates in two separate cohorts from respiratory disease outbreaks. The real-time PCR assay had a wide dynamic range, detecting from 102 to 107 copies of genomic DNA per reaction. The assay did not cross-react with other adenoviruses, influenza, respiratory syncytial virus, or common respiratory tract bacteria. The described assay is easy to use, sensitive and specific for HAdV-14a in clinical throat swab specimens, and very rapid since turnaround time is less than four hours to obtain an answer

Geographic origin and migration phenology of European red admirals (Vanessa atalanta) as revealed by stable isotopes.

BACKGROUND: Long-distance migration has evolved multiple times in different animal taxa. For insect migrants, the complete annual migration cycle covering several thousand kilometres, may be performed by several generations, each migrating part of the distance and reproducing. Different life-cycle stages and preferred orientation may thus, be found along the migration route. For migrating red admirals (Vanessa atalanta) it has been questioned if they reproduce in the most northern part of the range. Here we present migration phenology data from a two-year time series of migrating red admirals captured at Rybachy, Kaliningrad, in the northern part of Europe investigating time for migration, life-history stage (migration, reproduction) as well as site of origin in individual butterflies. METHODS: Red admirals were captured daily at a coastal site during spring, summer and autumn in 2004 and 2005. For the sampled individuals, reproductive status and fuel content were estimated by visual inspection, and hydrogen isotopes (δ 2H) were analysed in wing samples. δ 2H values was compared with samples from two nearby reference sites in Estonia and Poland. RESULTS: Analysis of hydrogen isotopes (δ 2H) in red admiral wings showed that the spring cohort were of a southerly origin, while those caught in August or later in the autumn were from the local region or areas further to the north. All females caught during spring had developing eggs in their abdomen, but no eggs were found in late summer/autumn. There was a male-biased sex ratio during autumn and a difference in lipid content between years. When comparing the isotopic data with inland nearby locations, it was clear that the range of δ 2H values (- 181 to - 78) was wider at Rybachy as compared to the two reference sites in Estonia and Poland (- 174 to - 100). CONCLUSIONS: During spring, migratory female red admirals arrived from the south and were ready to reproduce, while the autumn passage mainly engaged local and more northern individuals carrying large fuel deposits in preparation for long-distance migration. The phenology data suggest that individuals select to migrate in favourable weather conditions and that numbers may differ between years. Future studies should focus on individual sampling at a wide range of sites to reveal differential migration strategies and timing of migration between sexes and populations of migrating butterflies

Investigation of the Enteric Pathogenic Potential of Oral Campylobacter concisus Strains Isolated from Patients with Inflammatory Bowel Disease

BACKGROUND: Campylobacter concisus, a bacterium colonizing the human oral cavity, has been shown to be associated with inflammatory bowel disease (IBD). This study investigated if patients with IBD are colonized with specific oral C. concisus strains that have potential to cause enteric diseases. METHODOLOGY: Seventy oral and enteric C. concisus isolates obtained from eight patients with IBD and six controls were examined for housekeeping genes by multilocus sequence typing (MLST), Caco2 cell invasion by gentamicin-protection-assay, protein analysis by mass spectrometry and SDS-PAGE, and morphology by scanning electron microscopy. The whole genome sequenced C. concisus strain 13826 which was isolated from an individual with bloody diarrhea was included in MLST analysis. PRINCIPAL FINDINGS: MLST analysis showed that 87.5% of individuals whose C. concisus belonged to Cluster I had inflammatory enteric diseases (six IBD and one with bloody diarrhea), which was significantly higher than that in the remaining individuals (28.6%) (P<0.05). Enteric invasive C. concisus (EICC) oral strain was detected in 50% of patients with IBD and none of the controls. All EICC strains were in Cluster 1. The C. concisus strain colonizing intestinal tissues of patient No. 1 was closely related to the oral C. concisus strain from patient No. 6 and had gene recombination with the patient's own oral C. concisus. The oral and intestinal C. concisus strains of patient No. 3 were the same strain. Some individuals were colonized with multiple oral C. concisus strains that have undergone natural recombination. CONCLUSIONS: This study provides the first evidence that patients with IBD are colonized with specific oral C. concisus strains, with some being EICC strains. C. concisus colonizing intestinal tissues of patients with IBD at least in some instances results from an endogenous colonization of the patient's oral C. concisus and that C. concisus strains undergo natural recombination

Diversification across an altitudinal gradient in the Tiny Greenbul (Phyllastrephus debilis) from the Eastern Arc Mountains of Africa

<p>Abstract</p> <p>Background</p> <p>The Eastern Arc Mountains of Africa have become one of the focal systems with which to explore the patterns and mechanisms of diversification among montane species and populations. One unresolved question is the extent to which populations inhabiting montane forest interact with those of adjacent lowland forest abutting the coast of eastern Africa. The Tiny Greenbul (<it>Phyllastephus debilis</it>) represents the only described bird species within the Eastern Arc/coastal forest mosaic, which is polytypic across an altitudinal gradient: the subspecies <it>albigula </it>(green head) is distributed in the montane Usambara and Nguru Mountains whereas the subspecies <it>rabai </it>(grey head) is found in Tanzanian lowland and foothill forest. Using a combination of morphological and genetic data, we aim to establish if the pattern of morphological differentiation in the Tiny Greenbul (<it>Phyllastrephus debilis</it>) is the result of disruptive selection along an altitudinal gradient or a consequence of secondary contact following population expansion of two differentiated lineages.</p> <p>Results</p> <p>We found significant biometric differences between the lowland (<it>rabai</it>) and montane (<it>albigula</it>) populations in Tanzania. The differences in shape are coupled with discrete differences in the coloration of the underparts. Using multi-locus data gathered from 124 individuals, we show that lowland and montane birds form two distinct genetic lineages. The divergence between the two forms occurred between 2.4 and 3.1 Myrs ago.</p> <p>Our coalescent analyses suggest that limited gene flow, mostly from the subspecies <it>rabai </it>to <it>albigula</it>, is taking place at three mid-altitude localities, where lowland and montane rainforest directly abut. The extent of this introgression appears to be limited and is likely a consequence of the recent expansion of <it>rabai </it>further inland.</p> <p>Conclusion</p> <p>The clear altitudinal segregation in morphology found within the Tiny Greenbul is the result of secondary contact of two highly differentiated lineages rather than disruptive selection in plumage pattern across an altitudinal gradient. Based on our results, we recommend <it>albigula </it>be elevated to species rank.</p

Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically–relevant faecal environment, with implications for pathogenicity

Abstract Clostridium difficile virulence is driven primarily by the processes of toxinogenesis and sporulation, however many in vitro experimental systems for studying C. difficile physiology have arguably limited relevance to the human colonic environment. We therefore created a more physiologically–relevant model of the colonic milieu to study gut pathogen biology, incorporating human faecal water (FW) into growth media and assessing the physiological effects of this on C. difficile strain 630. We identified a novel set of C. difficile–derived metabolites in culture supernatants, including hexanoyl– and pentanoyl–amino acid derivatives by LC-MSn. Growth of C. difficile strain 630 in FW media resulted in increased cell length without altering growth rate and RNA sequencing identified 889 transcripts as differentially expressed (p < 0.001). Significantly, up to 300–fold increases in the expression of sporulation–associated genes were observed in FW media–grown cells, along with reductions in motility and toxin genes’ expression. Moreover, the expression of classical stress–response genes did not change, showing that C. difficile is well–adapted to this faecal milieu. Using our novel approach we have shown that interaction with FW causes fundamental changes in C. difficile biology that will lead to increased disease transmissibility

A method for real-time classification of insect vectors of mosaic and brown streak disease in cassava plants for future implementation within a low-cost, handheld, in-field multispectral imaging sensor

Background The paper introduces a multispectral imaging system and data-processing approach for the identification and discrimination of morphologically indistinguishable cryptic species of the destructive crop pest, the whitefly Bemisia tabaci. This investigation and the corresponding system design, was undertaken in two phases under controlled laboratory conditions. The first exploited a prototype benchtop variant of the proposed sensor system to analyse four cryptic species of whitefly reared under similar conditions. The second phase, of the methodology development, employed a commercial high-precision laboratory hyperspectral imager to recover reference data from five cryptic species of whitefly, immobilized through flash freezing, and taken from across four feeding environments. Results The initial results, for the single feeding environment, showed that a correct species classification could be achieved in 85–95% of cases, utilising linear Partial Least Squares approaches. The robustness of the classification approach was then extended both in terms of the automated spatial extraction of the most pertinent insect body parts, to assist with the spectral classification model, as well as the incorporation of a non-linear Support Vector Classifier to maintain the overall classification accuracy at 88–98%, irrespective of the feeding and crop environment. Conclusion This study demonstrates that through an integration of both the spatial data, associated with the multispectral images being used to separate different regions of the insect, and subsequent spectral analysis of those sub-regions, that B. tabaci viral vectors can be differentiated from other cryptic species, that appear morphologically indistinguishable to a human observer, with an accuracy of up to 98%. The implications for the engineering design for an in-field, handheld, sensor system is discussed with respect to the learning gained from this initial stage of the methodology development

Acoustic telemetry reveals strong spatial preferences and mixing during successive spawning periods in a partially migratory common bream population

Partial migration, whereby a population comprises multiple behavioural phenotypes that each have varying tendencies to migrate, is common among many animals. Determining the mechanisms by which these phenotypes are maintained is important for understanding their roles in population structure and stability. The aim here was to test for the temporal and spatial consistency of migratory phenotypes in a common bream Abramis brama (‘bream’) population, and then determine their social preferences and extent of mixing across three successive annual spawning periods. The study applied passive acoustic telemetry to track the movements of bream in the River Bure system of the Norfolk Broads, a lowland wetland comprising highly connected riverine and lacustrine habitats. Analyses revealed that individual migratory phenotype was highly consistent across the three years, but this was not predicted by fish sex or length at tagging. During the annual spawning periods, network analyses identified off-channel areas visited by both resident and migrant fish that, in non-spawning periods, were relatively independent in their space use. Within these sites, the co-occurrence of bream was non-random, with individuals forming more preferred and avoided associations than expected by chance. These associations were not strongly predicted by similarity in fish length, sex or behavioural phenotype, indicating that the resident and migrant phenotypes mixed during their annual spawning periods. The results suggested these different phenotypes, with spatially distinct resource use in non-spawning periods, comprised a single metapopulation, with this having important implications for the management of this wetland resource