Multiplex Touchdown PCR for Rapid Typing of the Opportunistic Pathogen Propionibacterium acnes

The opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA(1), IA(2), IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA(1), IA(2), and IC), sodA (types IA(2) and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA(1) (n = 145), IA(2) (n = 20), IB (n = 65), IC (n = 7), II (n = 45), and III (n = 30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses

An expanded multilocus sequence typing scheme for propionibacterium acnes : investigation of 'pathogenic', 'commensal' and antibiotic resistant strains

The Gram-positive bacterium Propionibacterium acnes is a member of the normal human skin microbiota and is associated with various infections and clinical conditions. There is tentative evidence to suggest that certain lineages may be associated with disease and others with health. We recently described a multilocus sequence typing scheme (MLST) for P. acnes based on seven housekeeping genes (http://pubmlst.org/pacnes). We now describe an expanded eight gene version based on six housekeeping genes and two ‘putative virulence’ genes (eMLST) that provides improved high resolution typing (91eSTs from 285 isolates), and generates phylogenies congruent with those based on whole genome analysis. When compared with the nine gene MLST scheme developed at the University of Bath, UK, and utilised by researchers at Aarhus University, Denmark, the eMLST method offers greater resolution. Using the scheme, we examined 208 isolates from disparate clinical sources, and 77 isolates from healthy skin. Acne was predominately associated with type IA1 clonal complexes CC1, CC3 and CC4; with eST1 and eST3 lineages being highly represented. In contrast, type IA2 strains were recovered at a rate similar to type IB and II organisms. Ophthalmic infections were predominately associated with type IA1 and IA2 strains, while type IB and II were more frequently recovered from soft tissue and retrieved medical devices. Strains with rRNA mutations conferring resistance to antibiotics used in acne treatment were dominated by eST3, with some evidence for intercontinental spread. In contrast, despite its high association with acne, only a small number of resistant CC1 eSTs were identified. A number of eSTs were only recovered from healthy skin, particularly eSTs representing CC72 (type II) and CC77 (type III). Collectively our data lends support to the view that pathogenic versus truly commensal lineages of P. acnes may exist. This is likely to have important therapeutic and diagnostic implications

Archäologische Prospektionen im Brüniggebiet - Vorbericht zur Prospektionskampagne 2014 in Lungern (OW) und Meiringen (BE)

Das Bronzemesser lag – wie auch ein Teil der mittelalterlichen Silberpfennige und verschiedene im Jahr 2014 gefundene (früh-)neuzeitliche Metallobjekte – unmittelbar auf der Laubdecke, d.h. auf der Oberkante des humosen Oberbodens (Ah-Horizont). Dies zeigt, dass die Bodenbildungsprozesse im Brüniggebiet äusserst langsam verlaufen und sich deswegen unterschiedlich alte Fundobjekte oftmals im gleichen stratigraphischen Kontext finden. Bei einer der untersuchten Trockenmauerkonstruktion am Nordrand der Geländestufe könnten Lage, Befund und Funde dafür sprechen, dass es sich um eine der „Hütten“ bzw. „Wachthütten“ handeln könnte, die von den Unterwaldnern im Zusammenhang mit dem Grenzkonflikt im Jahre 1712 errichtet wurden. Wichtige Hinweise für die Interpretation und Einordnung der diesjährigen und und früheren Prospektionsergebnisse lieferte die Transkription und Analyse des „Plan und Grundriss von dem grossen Pass über den so genannten Breünig Berg“ des Ingenieurs und Artillerieoffiziers Samuel Bodmer aus dem Jahr 1712 – auch wenn sich die Lokalisierung der verschiedenen militärischen und zivilen Bauten im Einzelfall ein schwieriges Unterfangen bleibt. Im Sinne einer ganzheitlichen Betrachtung der archäologisch-historischen Situation im Bereich des Brünig wurde im Berichtsjahr erstmals und mit Erfolg auch auf dem Gebiet der Gemeinde Meiringen (BE) prospektiert und erste Vorarbeiten und Abklärungen im Hinblick auf die geplante Dokumentation der erstaunlich gut erhaltenen Überreste des zwischen 1712 und 1714 errichteten „Schäntzli Nydegg“ durchgeführt

Syntax-based data augmentation for Hungarian-English machine translation

We train Transformer-based neural machine translation models for Hungarian-English and English-Hungarian using the Hunglish2 corpus. Our best models achieve a BLEU score of 40.0 on HungarianEnglish and 33.4 on English-Hungarian. Furthermore, we present results on an ongoing work about syntax-based augmentation for neural machine translation. Both our code and models are publicly available

Data Augmentation for Machine Translation via Dependency Subtree Swapping

We present a generic framework for data augmentation via dependency subtree swapping that is applicable to machine translation. We extract corresponding subtrees from the dependency parse trees of the source and target sentences and swap these across bisentences to create augmented samples. We perform thorough filtering based on graphbased similarities of the dependency trees and additional heuristics to ensure that extracted subtrees correspond to the same meaning. We conduct resource-constrained experiments on 4 language pairs in both directions using the IWSLT text translation datasets and the Hunglish2 corpus. The results demonstrate consistent improvements in BLEU score over our baseline models in 3 out of 4 language pairs. Our code is available on GitHub

Data augmentation for machine translation via dependency subtree swapping

We present a generic framework for data augmentation via dependency subtree swapping that is applicable to machine translation. We extract corresponding subtrees from the dependency parse trees of the source and target sentences and swap these across bisentences to create augmented samples. We perform thorough filtering based on graphbased similarities of the dependency trees and additional heuristics to ensure that extracted subtrees correspond to the same meaning. We conduct resource-constrained experiments on 4 language pairs in both directions using the IWSLT text translation datasets and the Hunglish2 corpus. The results demonstrate consistent improvements in BLEU score over our baseline models in 3 out of 4 language pairs. Our code is available on GitHub

Herschel/HIFI Spectral Mapping of C+^+, CH+^+, and CH in Orion BN/KL: The Prevailing Role of Ultraviolet Irradiation in CH+^+ Formation

The CH$^+$ ion is a key species in the initial steps of interstellar carbon chemistry. Its formation in diverse environments where it is observed is not well understood, however, because the main production pathway is so endothermic (4280 K) that it is unlikely to proceed at the typical temperatures of molecular clouds. We investigation CH$^+$ formation with the first velocity-resolved spectral mapping of the CH$^+$ $J=1-0, 2-1$ rotational transitions, three sets of CH $\Lambda$-doubled triplet lines, $^{12}$C$^+$ and $^{13}$C$^+$, and CH$_3$OH 835~GHz E-symmetry Q branch transitions, obtained with Herschel/HIFI over $\approx$12 arcmin$^2$ centered on the Orion BN/KL source. We present the spatial morphologies and kinematics, cloud boundary conditions, excitation temperatures, column densities, and $^{12}$C$^+$ optical depths. Emission from C$^+$, CH$^+$, and CH is indicated to arise in the diluted gas, outside of the explosive, dense BN/KL outflow. Our models show that UV-irradiation provides favorable conditions for steady-state production of CH$^+$ in this environment. Surprisingly, no spatial or kinematic correspondences of these species are found with H$_2$ S(1) emission tracing shocked gas in the outflow. We propose that C$^+$ is being consumed by rapid production of CO to explain the lack of C$^+$ and CH$^+$ in the outflow, and that fluorescence provides the reservoir of H$_2$ excited to higher ro-vibrational and rotational levels. Hence, in star-forming environments containing sources of shocks and strong UV radiation, a description of CH$^+$ formation and excitation conditions is incomplete without including the important --- possibly dominant --- role of UV irradiation.Comment: Accepted for publication in The Astrophysical Journa

Valoriser, optimiser, autonomiser: information literacy dans la formation du Bachelor en Travail social de la HES-SO

L’étude, mandatée par la filière Travail social de la Haute école de Travail social de Genève, a eu deux objectifs principaux : d’abord réfléchir sur la place de l’information literacy dans la formation de bachelor en Travail social de la Haute école spécialisée de Suisse occidentale (HES-SO) ; ensuite avancer des pistes de solutions pour la valorisation de l’IL et pour l’optimisation de son enseignement. Pour ce faire, elle a proposé une revue de la littérature, une enquête qualitative auprès des parties prenantes de la formation, ainsi que l’analyse comparative du référentiel de compétences et du concept pédagogique du PEC 2006 avec deux référentiels métiers du TS, deux référentiels de compétences informationnelles de l’enseignement supérieur et de six plans d’études BATS suisses, français et candiens. Les résultats de l’étude ont démontré l’importance de l’information literacy pour la pratique et pour la formation du Travail social. Le rôle des professionnel-le-s du Travail social en tant que facilitatrices de l’accès à l’information qui les confronte à la problématique de l’inégalité devant l’information a particulièrement été mis en lumière. Des enjeux informationnels actuels du Travail social qui nécessitent l’acquisition de nouvelles compétences ou la mobilisation des compétences « classiques » à un niveau d’expertise élevé ont également été identifiés. L’étude a confirmé l’importance de visibiliser la transversalité des compétences informationnelles à la fois dans le référentiel de compétences et dans la structure des études. Bien que les compétences informationnelles figurent en grand nombre dans le PEC 2006 et que leur formation soit en partie assurée, une optimisation de leur présentation dans une vision holistique est donc souhaitable. L’étude a abouti à la proposition d’un modèle de référentiel de compétences, d’un modèle de formations et d’un modèle de référentiel de formation. Après des analyses coûts/bénéfices et SWOT de l’élaboration d’une réforme conjointe du référentiel et de la formation jusqu’à sa formalisation officielle, elle présente un calendrier priorisé à court, à moyen et à long terme des recommandations concrètes pour le domaine Travail social de la HES-SO