Dynamic microsatellites in transcribed regions of gastropod mitochondrial 16S rDNA

Length variations of repetitive sequences in different AT-rich loop-coding regions of mitochondrial 16S rDNA in two gastropod species were discovered during intraspecific haplotype surveys. Examination of the discrete length variation of the basic repeat unit in a phylogenetic framework led to the conclusion of a microsatellite-like mutational dynamic. The observations suggest that the presence of a repetitive sequence structure alone is sufficient to trigger this dynamic.Des variations quant à la longueur de séquences répétitives au sein de diverses régions codantes à boucle AT-riche du gène codant pour l’ADNr 16S mitochondrial ont été découvertes chez deux gastéropodes lors de la comparaison d’haplotypes interspécifiques. Le fait que cette variation de taille, de type discrète, impliquait la perte ou le gain de monomères de la séquence répétitive a été interprété dans un contexte phylogénétique. Il en ressort que cette variation s’apparente à une dynamique mutationnelle analogue à celle des microsatellites. Ces observations suggèrent que la présence d’une structure formée de séquences répétitives suffit, à elle seule, à enclencher ce genre de dynamique. Mots clés : microsatellites, ARNr 16S, génome mitochondrial, ADN répétitif, gastéropodes

An integral equation approach for electromagnetic scattering by biperiodic structures

The objective of this paper is the analytical investigation of an integral equation formulation for electromagnetic scattering by 2&\pi;-biperiodic multilayered structures with polyhedral Lipschitz regular interfaces. Extending the combined potential ansatz from Preprint No. 1882 for the electric fields in the before mentioned electromagnetic scattering problem from single to N profile scattering yields an equivalent system of N integral equations. We present a uniqueness and two existence results for this system depending on the values of the electromagnetic material parameters of the considered biperiodic scatterer. This in particular includes the proof that the system of integral equations is of zero Fredholm index. The general case that the grating interfaces are of polyhedral Lipschitz regularity requires more strict assumptions than the special case of smooth grating interfaces. We exploit the solvability results of this work in a subsequent paper featuring a recursive integral equation algorithm for the 2π-biperiodic multilayered electromagnetic scattering problem

Analytical investigation of an integral equation method for electromagnetic scattering by biperiodic structures

This paper is concerned with the study of a new integral equation formulation for electromagnetic scattering by a 2π-biperiodic polyhedral Lipschitz profile. Using a combined potential ansatz, we derive a singular integral equation with Fredholm operator of index zero from time-harmonic Maxwell's equations and prove its equivalence to the electromagnetic scattering problem. Moreover, under certain assumptions on the electric permittivity and the magnetic permeability, we obtain existence and uniqueness results in the special case that the grating is smooth and, under more restrictive assumptions, in the case that the grating is of polyhedral Lipschitz regularity

Electromagnetic scattering by biperiodic multilayered gratings: A recursive integral equation approach

In this paper, we propose a new recursive integral equation algorithm to solve the direct problem of electromagnetic scattering by biperiodic multilayered structures with polyhedral Lipschitz regular interfaces. We work with a combined potential approach that involves one unknown density on each of the grating profiles of the multilayered scatterer. Justified by the transmission conditions of the underlying electromagnetic scattering problem, we assume that densities in adjacent layers are linearly linked by a boundary integral operator and derive a recursion for these densities. It comprehends the inversion of one boundary integral equation on each scattering interface. Our algorithm is shown to be equivalent to the biperiodic multilayered electromagnetic scattering problem. Moreover, we obtain new existence and uniqueness results for our recursive integral equation algorithm, which promises to lead to an efficient numerical implementation of the considered scattering problem. These solvability results depend on the regularity of the grating interfaces and the values of the electromagnetic material parameters of the biperiodic multilayered structure at hand

Generalizing Cross-Document Event Coreference Resolution Across Multiple Corpora

Cross-document event coreference resolution (CDCR) is an NLP task in which mentions of events need to be identified and clustered throughout a collection of documents. CDCR aims to benefit downstream multi-document applications, but despite recent progress on corpora and system development, downstream improvements from applying CDCR have not been shown yet. We make the observation that every CDCR system to date was developed, trained, and tested only on a single respective corpus. This raises strong concerns on their generalizability -- a must-have for downstream applications where the magnitude of domains or event mentions is likely to exceed those found in a curated corpus. To investigate this assumption, we define a uniform evaluation setup involving three CDCR corpora: ECB+, the Gun Violence Corpus and the Football Coreference Corpus (which we reannotate on token level to make our analysis possible). We compare a corpus-independent, feature-based system against a recent neural system developed for ECB+. Whilst being inferior in absolute numbers, the feature-based system shows more consistent performance across all corpora whereas the neural system is hit-and-miss. Via model introspection, we find that the importance of event actions, event time, etc. for resolving coreference in practice varies greatly between the corpora. Additional analysis shows that several systems overfit on the structure of the ECB+ corpus. We conclude with recommendations on how to achieve generally applicable CDCR systems in the future -- the most important being that evaluation on multiple CDCR corpora is strongly necessary. To facilitate future research, we release our dataset, annotation guidelines, and system implementation to the public.Comment: Accepted at CL Journa

Molekulare Systematik und Phylogeographie der Formengruppe Ancylus fluviatilis O. F. Müller 1774

Ziel dieser Dissertation war es, die genetische Variation innerhalb der Formengruppe Ancylus fluviatilis (Gastropoda: Basommatophora) zu untersuchen, und eine auf molekula­ ren Markern basierende Phylogenie zu erstellen. Die phylogenetischen Untersuchungen beinhalteten auch die Stellung der Familie Ancylidae innerhalb der Basommatophora. Außerdem wurde die geographische Verteilung der genetischen Variation untersucht und die phylogeographischen Prozesse, die zu dieser Verteilung geführt haben, analysiert. Die gefundene genetische Konstitution wurde im Zusammenhang mit bereits vorhandenen Daten über chromosomale und fortpflanzungsbiologische Besonderheiten von A. fluviatilis diskutiert. Für 147 Individuen aus 62 Populationen des gesamten Verbreitungsgebiets von A. fluviatilis wurden mitochondriale 16S rDNA­Sequenzen ermittelt. Es konnten 67 Haplotypen unterschieden werden. Die Haplotypen zeigen eine große genetische Diversität innerhalb der Formengruppe (bis zu 8.2% paarweise Sequenzdivergenz). Es lassen sich neun genetisch stark divergente Linien unterscheiden. In einer Population konnten dynamische dinukleotide Mikrosatelliten in der mtDNA­Sequenz nachgewiesen werden, die eine Längenvariation von vier­ bis achtfachem Grundmuster aufweisen. Als wahr­ scheinlicher Mechanismus für diese Längenvariation wird "slipped­strand­mispairing" angenommen. Mit Hilfe von nukleären RAPD­Markern wurde die genetische Trennung der mitochon­ drialen Linien bei syntop vorkommenden Linien auch auf nukleärer Ebene nachgewiesen. Die Formengruppe A. fluviatilis setzt sich somit aus einem Komplex reproduktiv isolierter Linien zusammen. Im Zusammenhang mit der bereits nachgewiesenen allotetraploiden Konstitution zumindest einer Linie und der resultierenden hohen Selbstbefruchtungsrate sind sowohl sympatrische als auch allopatrische Diversifizierungsereignisse für die Differenzierung der Linien verantwortlich. Drei der neun genetischen Linien sind geographisch weitverbreitet und kommen zum Teil syntop vor. Phylogeographische Analysen anhand von "nested clades" zeigten, daß isolation by distance zwar das Grundmuster für die Verbreitung von A. fluviatilis darstellt, daß dieses aber durch Expansionsereignisse, die die Besiedlung über weite Distanzen einschließen, überlagert sein kann. Zeitliche Abschätzungen ergaben für die Formengruppe A. fluviatilis ein Alter von mindestens 20 Millionen Jahren. Die rezent vorkommenden Linien sind schätzungsweise zwischen 8 und 14 Millionen Jahren alt. Für die phylogenetischen Untersuchungen innerhalb der Basommatophora wurde die 16S­ rDNA von weiteren Gattungen sequenziert. Die resultierende molekulare Phylogenie belegt die monophyletische Entstehung der Formengruppe A. fluviatilis sowie eine gemeinsame Abstammung der Gattungen Ferrissia und Ancylus. Die Familie Ancylidae bildet eine Schwestergruppe zur Familie Planorbidae und läßt sich somit nicht aus dieser ableiten. Die Gattung Burnupia zeigt sich als nahe verwandt zur Gattung Acroloxus (Familie Acroloxidae) und gehört somit nicht, wie bisher angenommen, zu den Ancylidae

Anti-inflammatory activity of Punica granatum L. (Pomegranate) rind extracts applied topically to ex vivo skin

Coadministered pomegranate rind extract (PRE) and zinc (II) produces a potent virucidal activity against Herpes simplex virus (HSV); however, HSV infections are also associated with localised inflammation and pain. Here, the objective was to determine the anti-inflammatory activity and relative depth penetration of PRE, total pomegranate tannins (TPT) and zinc (II) in skin, ex vivo. PRE, TPT and ZnSO4 were dosed onto freshly excised ex vivo porcine skin mounted in Franz diffusion cells and analysed for COX-2, as a marker for modulation of the arachidonic acid inflammation pathway, by Western blotting and immunohistochemistry. Tape stripping was carried out to construct relative depth profiles. Topical application of PRE to ex vivo skin downregulated expression of COX-2, which was significant after just 6 h, and maintained for up to 24 h. This was achieved with intact stratum corneum, proving that punicalagin penetrated skin, further supported by the depth profiling data. When PRE and ZnSO4 were applied together, statistically equal downregulation of COX-2 was observed when compared to the application of PRE alone; no effect followed the application of ZnSO4 alone. TPT downregulated COX-2 less than PRE, indicating that tannins alone may not be entirely responsible for the anti-inflammatory activity of PRE. Punicalagin was found throughout the skin, in particular the lower regions, indicating appendageal delivery as a significant route to the viable epidermis. Topical application of TPT and PRE had significant anti-inflammatory effects in ex vivo skin, confirming that PRE penetrates the skin and modulates COX-2 regulation in the viable epidermis. Pomegranates have potential as a novel approach in ameliorating the inflammation and pain associated with a range of skin conditions, including cold sores and herpetic stromal keratitis

Extensively drug-resistant New Delhi metallo-β-lactamase–encoding bacteria in the environment, Dhaka, Bangladesh, 2012

Carriage of the New Delhi metallo-β-lactamase variant 1 (NDM-1) enables drug resistance to move between communities and hospitals. In Bangladesh, we found the blaNDM-1 gene in 62% of environmental waters and in fermentative and nonfermentative gram-negative bacteria. Escherichia coli sequence type (ST) 101 was most commonly found, reflecting a common global relationship between ST101 and NDM-1