Helminth parasites secrete extracellular vesicles (EVs) that can be internalised by host immune cells resulting in modulation of host immunity. While the molecular cargo of EVs have been ...characterised in many parasites, little is known about the surface-exposed molecules that participate in ligand-receptor interactions with the host cell surface to initiate vesicle docking and subsequent internalisation. Using a membrane-impermeable biotin reagent to capture proteins displayed on the outer membrane surface of two EV sub-populations (termed 15k and 120k EVs) released by adult F. hepatica, we describe 380 surface proteins including an array of virulence factors, membrane transport proteins and molecules involved in EV biogenesis/trafficking. Proteomics and immunohistochemical analysis show that the 120k EVs have an endosomal origin and may be released from the parasite via the protonephridial (excretory) system whilst the larger 15k EVs are released from the gastrodermal epithelial cells that line the fluke gut. A parallel lectin microarray strategy was used to profile the topology of major surface oligosaccharides of intact fluorogenically-labelled EVs as they would be displayed to the host. Lectin profiles corresponding to glycoconjugates exposed on the surface of the 15 K and 120K EV sub-populations are practically identical but are distinct from those of the parasite surface tegument, although all are predominated by high mannose sugars. We found that while the F. hepatica EVs were resistant to exo- and endo-glycosidases, the glyco-amidase PNGase F drastically remodelled the surface oligosaccharides and blocked the uptake of EVs by host macrophages. In contrast, pre-treatment with antibodies obtained from infected hosts, or purified antibodies raised against the extracellular domains of specific EV surface proteins (DM9-containing protein, CD63 receptor and myoferlin), significantly enhanced their cellular internalisation. This work highlights the diversity of EV biogenesis and trafficking pathways used by F. hepatica and sheds light on the molecular interaction between parasite EVs and host cells.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Although modern machine learning has the potential to greatly speed up the interpretation of imagery, the varied nature of the seabed and limited availability of expert annotations form barriers to ...its widespread use in seafloor mapping applications. This motivates research into unsupervised methods that function without large databases of human annotations. This paper develops an unsupervised feature learning method for georeferenced seafloor visual imagery that considers patterns both within the footprint of a single image frame and broader scale spatial characteristics. Features within images are learnt using an autoencoder developed based on the AlexNet deep convolutional neural network. Features larger than each image frame are learnt using a novel loss function that regularises autoencoder training using the Kullback–Leibler divergence function to loosely assume that images captured within a close distance of each other look more similar than those that are far away. The method is used to semantically interpret images taken by an autonomous underwater vehicle at the Southern Hydrates Ridge, an active gas hydrate field and site of a seafloor cabled observatory at a depth of 780 m. The method's performance when applied to clustering and content‐based image retrieval is assessed against a ground truth consisting of more than 18,000 human annotations. The study shows that the location based loss function increases the rate of information retrieval by a factor of two for seafloor mapping applications. The effects of physics‐based colour correction and image rescaling are also investigated, showing that the improved consistency of spatial information achieved by rescaling is beneficial for recognising artificial objects such as cables and infrastructures, but is less effective for natural objects that have greater dimensional variability.
The recent discovery that parasites release extracellular vesicles (EVs) that can transfer a range of effector molecules to host cells has made us re-think our understanding of the host–parasite ...interface. In this opinion article we consider how recent proteomics and transcriptomics studies, together with ultrastructural observations, suggest that more than one mechanism of EV biogenesis can occur in helminths. We propose that distinct EV subtypes have roles in immune modulation and repair of drug-induced damage, and put forward the case for targeting EV biogenesis pathways to achieve parasite control. In doing so we raise a number of outstanding research questions that must be addressed before this can happen.
This paper identifies five distinct mechanisms by which a population-based algorithm might have an advantage over a solo-search algorithm in classical optimization. These mechanisms are illustrated ...through a number of toy problems. Simulations are presented comparing different search algorithms on these problems. The plausibility of these mechanisms occurring in classical optimization problems is discussed. The first mechanism we consider relies on putting together building blocks from different solutions. This is extended to include problems containing critical variables. The second mechanism is the result of focusing of the search caused by crossover. Also discussed in this context is strong focusing produced by averaging many solutions. The next mechanism to be examined is the ability of a population to act as a low-pass filter of the landscape, ignoring local distractions. The fourth mechanism is a population's ability to search different parts of the fitness landscape, thus hedging against bad luck in the initial position or the decisions it makes. The final mechanism is the opportunity of learning useful parameter values to balance exploration against exploitation.
This paper carries out a comparison of the fitness landscape for four classic optimization problems: Max-Sat, graph-coloring, traveling salesman, and quadratic assignment. We have focused on two ...types of properties, local average properties of the landscape, and properties of the local optima. For the local optima we give a fairly comprehensive description of the properties, including the expected time to reach a local optimum, the number of local optima at different cost levels, the distance between optima, and the expected probability of reaching the optima. Principle component analysis is used to understand the correlations between the local optima. Most of the properties that we examine have not been studied previously, particularly those concerned with properties of the local optima. We compare and contrast the behavior of the four different problems. Although the problems are very different at the low level, many of the long-range properties exhibit a remarkable degree of similarity.
The liver fluke,
, is an obligate blood-feeder, and the gastrodermal cells of the parasite form the interface with the host's blood. Despite their importance in the host-parasite interaction, ...in-depth proteomic analysis of the gastrodermal cells is lacking. Here, we used laser microdissection of
tissue sections to generate unique and biologically exclusive tissue fractions of the gastrodermal cells and tegument for analysis by mass spectrometry. A total of 226 gastrodermal cell proteins were identified, with proteases that degrade haemoglobin being the most abundant. Other detected proteins included those such as proton pumps and anticoagulants which maintain a microenvironment that facilitates digestion. By comparing the gastrodermal cell proteome and the 102 proteins identified in the laser microdissected tegument with previously published tegument proteomic datasets, we showed that one-quarter of proteins (removed by freeze-thaw extraction) or one-third of proteins (removed by detergent extraction) previously identified as tegumental were instead derived from the gastrodermal cells. Comparative analysis of the laser microdissected gastrodermal cells, tegument, and
secretome revealed that the gastrodermal cells are the principal source of secreted proteins, as well as showed that both the gastrodermal cells and the tegument are likely to release subpopulations of extracellular vesicles (EVs). Microscopical examination of the gut caeca from flukes fixed immediately after their removal from the host bile ducts showed that selected gastrodermal cells underwent a progressive thinning of the apical plasma membrane which ruptured to release secretory vesicles en masse into the gut lumen. Our findings suggest that gut-derived EVs are released via a novel atypical secretory route and highlight the importance of the gastrodermal cells in nutrient acquisition and possible immunomodulation by the parasite.
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•Extracellular vesicle (EV) biogenesis pathways are conserved in helminths.•However, ESCRT proteins may operate in a non-canonical manner.•Helminths display phylum-level divergence of ...EV RNA-loading machinery.
A comparative genomics approach was used to determine whether established extracellular vesicle biogenesis pathways are conserved in helminths. This revealed conservation of membrane and cytoskeletal organising proteins as well as the endosomal sorting complex required for transport previously described in mammalian cells. Domain level analysis of this complex in helminths, however, indicated that some species may rely on atypical proteins to support subunit interactions and cargo recruitment. Interestingly, helminths displayed phylum level divergence of proteins associated with loading RNA into extracellular vesicles. These findings provide a framework for functional studies of helminth extracellular vesicle biogenesis and cargo sorting.
•We provide detailed analysis of gray-sheep users problem in recommender systems.•We show how conventional collaborative filtering fail for gray-sheep users problem.•We use K-means clustering to ...separate these users from rest of the users.•We propose switching hybrid recommender system to overcome this problem.
Recommender systems apply data mining and machine learning techniques for filtering unseen information and can predict whether a user would like a given item. This paper focuses on gray-sheep users problem responsible for the increased error rate in collaborative filtering based recommender systems. This paper makes the following contributions: we show that (1) the presence of gray-sheep users can affect the performance – accuracy and coverage – of the collaborative filtering based algorithms, depending on the data sparsity and distribution; (2) gray-sheep users can be identified using clustering algorithms in offline fashion, where the similarity threshold to isolate these users from the rest of community can be found empirically. We propose various improved centroid selection approaches and distance measures for the K-means clustering algorithm; (3) content-based profile of gray-sheep users can be used for making accurate recommendations. We offer a hybrid recommendation algorithm to make reliable recommendations for gray-sheep users. To the best of our knowledge, this is the first attempt to propose a formal solution for gray-sheep users problem. By extensive experimental results on two different datasets (MovieLens and community of movie fans in the FilmTrust website), we showed that the proposed approach reduces the recommendation error rate for the gray-sheep users while maintaining reasonable computational performance.
Nonnegative matrix factorization (NMF) is primarily a linear dimensionality reduction technique that factorizes a nonnegative data matrix into two smaller nonnegative matrices: one that represents ...the basis of the new subspace and the second that holds the coefficients of all the data points in that new space. In principle, the nonnegativity constraint forces the representation to be sparse and parts based. Instead of extracting holistic features from the data, real parts are extracted that should be significantly easier to interpret and analyze. The size of the new subspace selects how many features will be extracted from the data. An effective choice should minimize the noise while extracting the key features. We propose a mechanism for selecting the subspace size by using a minimum description length technique. We demonstrate that our technique provides plausible estimates for real data as well as accurately predicting the known size of synthetic data. We provide an implementation of our code in a Matlab format.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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