The occurrence and characterization of Campylobacter jejuni and C. coli in organic pigs and their outdoor environment

The occurrence and species distribution of thermophilic Campylobacter was investigated in organic outdoor pigs. An increased exposure of outdoor pigs to C. jejuni from the environment may cause a shift from a normal dominance of C. coli to more C. jejuni, which may imply a concern of reduced food safety. Bacteriological methods for determination of Campylobacter excretion level were combined with colony-blot hybridization and real-time PCR for specific detection of C. jejuni in pigs. Campylobacter was isolated from pigs (n = 47), paddock environment (n = 126) and wildlife (n = 44), identified to species by real-time PCR and sub-typed by serotyping (Penner) and pulse-field gel electrophorsis (PFGE) genotyping. All pigs excreted Campylobacter (103–107 CFU g1 faeces) from the age of 8–13-weeks old. C. jejuni was found in 29% of pigs in three consecutive trials and always in minority to C. coli (0.3–46%). C. jejuni and C. coli were isolated from 10% and 29% of the environmental samples, respectively, while crow-birds and rats harboured C. jejuni. Individual pigs hosted several strains (up to nine serotypes). The paddock environment was contaminated with C. coli serotypes similar to pig isolates, while most of the C. jejuni serotypes differed. C. jejuni isolates of different origin comprised few similar serotypes, just one identical genotype was common between pigs, environment and birds. In conclusion, the occurrence of C. jejuni varied considerably between the three groups of outdoor pigs. Furthermore, transfer of C. jejuni to the outdoor pigs from the nearby environment was not predominant according to the subtype dissimilarities of the obtained isolates

Non-supersymmetric Tachyon-free Type-II and Type-I Closed Strings from RCFT

We consider non-supersymmetric four-dimensional closed string theories constructed out of tensor products of N=2 minimal models. Generically such theories have closed string tachyons, but these may be removed either by choosing a non-trivial partition function or a suitable Klein bottle projection. We find large numbers of examples of both types.Comment: 9 pages, 1 tabl

Superpotentials for M-theory on a G_2 holonomy manifold and Triality symmetry

For $M$-theory on the $G_2$ holonomy manifold given by the cone on {\bf S^3}\x {\bf S^3} we consider the superpotential generated by membrane instantons and study its transformations properties, especially under monodromy transformations and triality symmetry. We find that the latter symmetry is, essentially, even a symmetry of the superpotential. As in Seiberg/Witten theory, where a flat bundle given by the periods of an universal elliptic curve over the $u$-plane occurs, here a flat bundle related to the Heisenberg group appears and the relevant universal object over the moduli space is related to hyperbolic geometry.Comment: 58 pages, latex; references adde

Lectures on conformal field theory and Kac-Moody algebras

This is an introduction to the basic ideas and to a few further selected topics in conformal quantum field theory and in the theory of Kac-Moody algebras.Comment: 59 pages, LaTeX2e, extended version of lectures given at the Graduate Course on Conformal Field Theory and Integrable Models (Budapest, August 1996), to appear in Springer Lecture Notes in Physic

Boundary Liouville theory at c=1

The c=1 Liouville theory has received some attention recently as the Euclidean version of an exact rolling tachyon background. In an earlier paper it was shown that the bulk theory can be identified with the interacting c=1 limit of unitary minimal models. Here we extend the analysis of the c=1-limit to the boundary problem. Most importantly, we show that the FZZT branes of Liouville theory give rise to a new 1-parameter family of boundary theories at c=1. These models share many features with the boundary Sine-Gordon theory, in particular they possess an open string spectrum with band-gaps of finite width. We propose explicit formulas for the boundary 2-point function and for the bulk-boundary operator product expansion in the c=1 boundary Liouville model. As a by-product of our analysis we also provide a nice geometric interpretation for ZZ branes and their relation with FZZT branes in the c=1 theory.Comment: 37 pages, 1 figure. Minor error corrected, slight change in result (1.6

Inversion polymorphism in a complete human genome assembly

The telomere-to-telomere (T2T) complete human reference has significantly improved our ability to characterize genome structural variation. To understand its impact on inversion polymorphisms, we remapped data from 41 genomes against the T2T reference genome and compared it to the GRCh38 reference. We find a ~ 21% increase in sensitivity improving mapping of 63 inversions on the T2T reference. We identify 26 misorientations within GRCh38 and show that the T2T reference is three times more likely to represent the correct orientation of the major human allele. Analysis of 10 additional samples reveals novel rare inversions at chromosomes 15q25.2, 16p11.2, 16q22.1-23.1, and 22q11.21

Gaps and complex structurally variant loci in phased genome assemblies

There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation

Origins of the Ambient Solar Wind: Implications for Space Weather

The Sun's outer atmosphere is heated to temperatures of millions of degrees, and solar plasma flows out into interplanetary space at supersonic speeds. This paper reviews our current understanding of these interrelated problems: coronal heating and the acceleration of the ambient solar wind. We also discuss where the community stands in its ability to forecast how variations in the solar wind (i.e., fast and slow wind streams) impact the Earth. Although the last few decades have seen significant progress in observations and modeling, we still do not have a complete understanding of the relevant physical processes, nor do we have a quantitatively precise census of which coronal structures contribute to specific types of solar wind. Fast streams are known to be connected to the central regions of large coronal holes. Slow streams, however, appear to come from a wide range of sources, including streamers, pseudostreamers, coronal loops, active regions, and coronal hole boundaries. Complicating our understanding even more is the fact that processes such as turbulence, stream-stream interactions, and Coulomb collisions can make it difficult to unambiguously map a parcel measured at 1 AU back down to its coronal source. We also review recent progress -- in theoretical modeling, observational data analysis, and forecasting techniques that sit at the interface between data and theory -- that gives us hope that the above problems are indeed solvable.Comment: Accepted for publication in Space Science Reviews. Special issue connected with a 2016 ISSI workshop on "The Scientific Foundations of Space Weather." 44 pages, 9 figure