Vaccination against Clostridium difficile using toxin fragments: Observations and analysis in animal models

Clostridium difficile is a major cause of antibiotic associated diarrhea. Recently, we have shown that effective protection can be mediated in hamsters through the inclusion of specific recombinant fragments from toxin A and B in a systemically delivered vaccine. Interestingly while neutralizing antibodies to the binding domains of both toxin A and B are moderately protective, enhanced survival is observed when fragments from the glucosyltransferase region of toxin B replace those from the binding domain of this toxin. In this addendum, we discuss additional information that has been derived from such vaccination studies. This includes observations on efficacy and cross-protection against different ribotypes mediated by these vaccines and the challenges that remain for a vaccine which prevents clinical symptoms but not colonization. The use and value of vaccination both in the prevention of infection and for treatment of disease relapse will be discussed

Multitask Learning on Graph Neural Networks: Learning Multiple Graph Centrality Measures with a Unified Network

The application of deep learning to symbolic domains remains an active research endeavour. Graph neural networks (GNN), consisting of trained neural modules which can be arranged in different topologies at run time, are sound alternatives to tackle relational problems which lend themselves to graph representations. In this paper, we show that GNNs are capable of multitask learning, which can be naturally enforced by training the model to refine a single set of multidimensional embeddings $\in \mathbb{R}^d$ and decode them into multiple outputs by connecting MLPs at the end of the pipeline. We demonstrate the multitask learning capability of the model in the relevant relational problem of estimating network centrality measures, focusing primarily on producing rankings based on these measures, i.e. is vertex $v_1$ more central than vertex $v_2$ given centrality $c$?. We then show that a GNN can be trained to develop a \emph{lingua franca} of vertex embeddings from which all relevant information about any of the trained centrality measures can be decoded. The proposed model achieves $89\%$ accuracy on a test dataset of random instances with up to 128 vertices and is shown to generalise to larger problem sizes. The model is also shown to obtain reasonable accuracy on a dataset of real world instances with up to 4k vertices, vastly surpassing the sizes of the largest instances with which the model was trained ($n=128$). Finally, we believe that our contributions attest to the potential of GNNs in symbolic domains in general and in relational learning in particular.Comment: Published at ICANN2019. 10 pages, 3 Figure

Design and Experimental Characterization of a Niti-Based, High-Frequency, Centripetal Peristaltic Actuator

Development and experimental testing of a peristaltic device actuated by a single shape-memory NiTi wire are described. The actuator is designed to radially shrink a compliant silicone pipe, and must work on a sustained basis at an actuation frequency that is higher than those typical of NiTi actuators. Four rigid, aluminum-made circular sectors are sitting along the pipe circumference and provide the required NiTi wire housing. The aluminum assembly acts as geometrical amplifier of the wire contraction and as heat sink required to dissipate the thermal energy of the wire during the cooling phase. We present and discuss the full experimental investigation of the actuator performance, measured in terms of its ability to reduce the pipe diameter, at a sustained frequency of 1.5 Hz. Moreover, we investigate how the diameter contraction is affected by various design parameters as well as actuation frequencies up to 4 Hz. We manage to make the NiTi wire work at 3% in strain, cyclically providing the designed pipe wall displacement. The actuator performance is found to decay approximately linearly with actuation frequencies up to 4 Hz. Also, the interface between the wire and the aluminum parts is found to be essential in defining the functional performance of the actuator

Identification of a novel zinc metalloprotease through a global analysis of clostridium difficile extracellular proteins

Clostridium difficile is a major cause of infectious diarrhea worldwide. Although the cell surface proteins are recognized to be important in clostridial pathogenesis, biological functions of only a few are known. Also, apart from the toxins, proteins exported by C. difficile into the extracellular milieu have been poorly studied. In order to identify novel extracellular factors of C. difficile, we analyzed bacterial culture supernatants prepared from clinical isolates, 630 and R20291, using liquid chromatography-tandem mass spectrometry. The majority of the proteins identified were non-canonical extracellular proteins. These could be largely classified into proteins associated to the cell wall (including CWPs and extracellular hydrolases), transporters and flagellar proteins. Seven unknown hypothetical proteins were also identified. One of these proteins, CD630_28300, shared sequence similarity with the anthrax lethal factor, a known zinc metallopeptidase. We demonstrated that CD630_28300 (named Zmp1) binds zinc and is able to cleave fibronectin and fibrinogen in vitro in a zinc-dependent manner. Using site-directed mutagenesis, we identified residues important in zinc binding and enzymatic activity. Furthermore, we demonstrated that Zmp1 destabilizes the fibronectin network produced by human fibroblasts. Thus, by analyzing the exoproteome of C. difficile, we identified a novel extracellular metalloprotease that may be important in key steps of clostridial pathogenesis

Relaminarization by steady modification of the streamwise velocity profile in a pipe

We show that a rather simple, steady modification of the streamwise velocity profile in a pipe can lead to a complete collapse of turbulence and the flow fully relaminarizes. Two different devices, a stationary obstacle (inset) and a device to inject additional fluid through an annular gap close to the wall, are used to control the flow. Both devices modify the streamwise velocity profile such that the flow in the center of the pipe is decelerated and the flow in the near wall region is accelerated. We present measurements with stereoscopic particle image velocimetry to investigate and capture the development of the relaminarizing flow downstream these devices and the specific circumstances responsible for relaminarization. We find total relaminarization up to Reynolds numbers of 6000, where the pressure drop in the downstream distance is reduced by a factor of 3.4 due to relaminarization. In a smooth straight pipe the flow remains completely laminar downstream of the control. Furthermore, we show that transient (temporary) relaminarization in a spatially confined region right downstream the devices occurs also at much higher Reynolds numbers, accompanied by a significant drag reduction. The underlying physical mechanism of relaminarization is attributed to a weakening of the near-wall turbulence production cycle

Large-scale variability in style and magnitude of footwall rift-related unconformities, northern Carnarvon Basin, offshore NW Australia

Fault-scarp degradation complexes record rift-related erosion of normal fault scarps. At the scale of an individual fault segment, the magnitude and distribution of erosion are related to the total and along-strike variability in fault throw. However, previous studies on degradation complexes focused on one type of rift-related erosional unconformity, with the factors controlling the development, magnitude and style of footwall erosion at a far larger scale (i.e. several fault blocks) being poorly constrained. This study uses high-resolution subsurface data to constrain the timing, magnitude and style of footwall erosion across the NW Shelf of Australia. By doing so, we test conceptual and numerical model predictions for the development of rift-related unconformities. We show that development of footwall erosion complexes is dependent on the occurrence and duration of footwall exposure and that fault throw and footwall uplift control the magnitude of erosion. Furthermore, the style of footwall erosion depends on the driving process(es), with gravitational instabilities resulting in cuspate footwall crest erosional surfaces, whereas peneplain-style surfaces develop in response to wave-driven erosion dictated by the base level. The results of this study can help refine rift-related fault evolution and the effects of sea-level changes in tectonostratigraphic models of rift basins

Adhesion Improvement of Thermoplastics-Based Composites by Atmospheric Plasma and UV Treatments

The present work is concerned with adhesive bonding of thermoplastic composites used in general aerospace applications, including polyphenylene sulfide (PPS), polyetherimide (PEI) and polyetheretherketone (PEEK) carbon fibre composites. Three different surface treatments have been applied to the PEEK, PPS and PEI-based composites in order to enhance the adhesion: atmospheric plasma, ultraviolet radiation (UV) and isopropanol wiping as a control. Water contact angles and free surface energies were measured following the standard experimental procedure based on the employment of three different liquid droplets. Infrared spectroscopy and X-ray photoelectron spectroscopy (XPS) were subsequently performed to characterize the surface chemistry of the samples after treatment. The single lap joints were manufactured and bonded by an Aerospace grade epoxy-based film adhesive originally developed for use on metals but with the ability to bond treated thermoplastics to good strength (supplied by Henkel Ireland). Quasi-static (QS) tests were conducted. The lap shear strength was evaluated, and the failure mechanisms of the different joints were examined for the range of surface treatments considered. It was found that the performances of the PEEK and PPS joints were considerably improved by the plasma and UV treatments resulting in cohesive and delamination failures, while PEI was unaffected by the plasma and UV treatments and performed very well throughout

Cohabitation of settlements among crested porcupine (Hystrix cristata), red fox (Vulpes vulpes) and European badger (Meles meles)

In Italy, porcupines, badgers and red foxes share the same settlements. However, there is lack of informa-tion concerning their cohabitation. From 2012 to 2019, cohabitation by these three mammals was studied using camera-trapping and was found to occur only between porcupines and badgers, even in the presence of porcupettes. Cohabitation was associated with aggressive interaction between porcupines and badg-ers. Foxes were found to be scavengers of porcupine carcasses. Cohabitation among these semi-fossorial mammals and scavenging behaviour could play a role in disease transmission, including zoonotic diseases

Super-resolution imaging as a method to study GPCR dimers and higher-order oligomers

The study of G protein-coupled receptor (GPCR) dimers and higher-order oligomers has unveiled mechanisms for receptors to diversify signaling and potentially uncover novel therapeutic targets. The functional and clinical significance of these receptor–receptor associations has been facilitated by the development of techniques and protocols, enabling researchers to unpick their function from the molecular interfaces, to demonstrating functional significance in vivo, in both health and disease. Here we describe our methodology to study GPCR oligomerization at the single-molecule level via super-resolution imaging. Specifically, we have employed photoactivated localization microscopy, with photoactivatable dyes (PD-PALM) to visualize the spatial organization of these complexes to <10 nm resolution, and the quantitation of GPCR monomer, dimer, and oligomer in both homomeric and heteromeric forms. We provide guidelines on optimal sample preparation, imaging parameters, and necessary controls for resolving and quantifying single-molecule data. Finally, we discuss advantages and limitations of this imaging technique and its potential future applications to the study of GPCR function