1,921 research outputs found
BlogForever D2.6: Data Extraction Methodology
This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform
An antibody raised against a pathogenic serpin variant induces mutant-like behaviour in the wild-type protein
A monoclonal antibody (mAb) that binds to a transient intermediate may act as a catalyst for the corresponding reaction; here we show this principle can extend on a macro molecular scale to the induction of mutant-like oligomerization in a wild-type protein. Using the common pathogenic E342K (Z) variant of α1-antitrypsin as antigen-whose native state is susceptible to the formation of a proto-oligomeric intermediate-we have produced a mAb (5E3) that increases the rate of oligomerization of the wild-type (M) variant. Employing ELISA, gel shift, thermal stability and FRET time-course experiments, we show that mAb5E3 does not bind to the native state of α1-antitrypsin, but recognizes a cryptic epitope in the vicinity of the post-helix A loop and strand 4C that is revealed upon transition to the polymerization intermediate, and which persists in the ensuing oligomer. This epitope is not shared by loop-inserted monomeric conformations. We show the increased amenity to polymerization by either the pathogenic E342K mutation or the binding of mAb5E3 occurs without affecting the energetic barrier to polymerization. As mAb5E3 also does not alter the relative stability of the monomer to intermediate, it acts in a manner similar to the E342K mutant, by facilitating the conformational interchange between these two states
Nature of the spin-glass phase at experimental length scales
We present a massive equilibrium simulation of the three-dimensional Ising
spin glass at low temperatures. The Janus special-purpose computer has allowed
us to equilibrate, using parallel tempering, L=32 lattices down to T=0.64 Tc.
We demonstrate the relevance of equilibrium finite-size simulations to
understand experimental non-equilibrium spin glasses in the thermodynamical
limit by establishing a time-length dictionary. We conclude that
non-equilibrium experiments performed on a time scale of one hour can be
matched with equilibrium results on L=110 lattices. A detailed investigation of
the probability distribution functions of the spin and link overlap, as well as
of their correlation functions, shows that Replica Symmetry Breaking is the
appropriate theoretical framework for the physically relevant length scales.
Besides, we improve over existing methodologies to ensure equilibration in
parallel tempering simulations.Comment: 48 pages, 19 postscript figures, 9 tables. Version accepted for
publication in the Journal of Statistical Mechanic
Thermodynamic glass transition in a spin glass without time-reversal symmetry
Spin glasses are a longstanding model for the sluggish dynamics that appears
at the glass transition. However, spin glasses differ from structural glasses
for a crucial feature: they enjoy a time reversal symmetry. This symmetry can
be broken by applying an external magnetic field, but embarrassingly little is
known about the critical behaviour of a spin glass in a field. In this context,
the space dimension is crucial. Simulations are easier to interpret in a large
number of dimensions, but one must work below the upper critical dimension
(i.e., in d<6) in order for results to have relevance for experiments. Here we
show conclusive evidence for the presence of a phase transition in a
four-dimensional spin glass in a field. Two ingredients were crucial for this
achievement: massive numerical simulations were carried out on the Janus
special-purpose computer, and a new and powerful finite-size scaling method.Comment: 10 pages, 6 figure
Optimizing street mobility through a netlogo simulation environment
The routes and streets make it possible to drive and travel through the cities, but unfortunately traffic and particularly congestion leads to drivers losing time while traveling from one place to another, because of the time it takes to transit on the roads, in addition to waiting times by traffic lights. This research introduces the extension of an agent-oriented system aimed at reducing driver waiting times at a street intersection. The simulation environment was implemented in NetLogo, which allowed comparison of the impact of Smart traffic light use versus a fixed-time traffic light
Janus II: a new generation application-driven computer for spin-system simulations
This paper describes the architecture, the development and the implementation
of Janus II, a new generation application-driven number cruncher optimized for
Monte Carlo simulations of spin systems (mainly spin glasses). This domain of
computational physics is a recognized grand challenge of high-performance
computing: the resources necessary to study in detail theoretical models that
can make contact with experimental data are by far beyond those available using
commodity computer systems. On the other hand, several specific features of the
associated algorithms suggest that unconventional computer architectures, which
can be implemented with available electronics technologies, may lead to order
of magnitude increases in performance, reducing to acceptable values on human
scales the time needed to carry out simulation campaigns that would take
centuries on commercially available machines. Janus II is one such machine,
recently developed and commissioned, that builds upon and improves on the
successful JANUS machine, which has been used for physics since 2008 and is
still in operation today. This paper describes in detail the motivations behind
the project, the computational requirements, the architecture and the
implementation of this new machine and compares its expected performances with
those of currently available commercial systems.Comment: 28 pages, 6 figure
The three dimensional Ising spin glass in an external magnetic field: the role of the silent majority
We perform equilibrium parallel-tempering simulations of the 3D Ising
Edwards-Anderson spin glass in a field. A traditional analysis shows no signs
of a phase transition. Yet, we encounter dramatic fluctuations in the behaviour
of the model: Averages over all the data only describe the behaviour of a small
fraction of it. Therefore we develop a new approach to study the equilibrium
behaviour of the system, by classifying the measurements as a function of a
conditioning variate. We propose a finite-size scaling analysis based on the
probability distribution function of the conditioning variate, which may
accelerate the convergence to the thermodynamic limit. In this way, we find a
non-trivial spectrum of behaviours, where a part of the measurements behaves as
the average, while the majority of them shows signs of scale invariance. As a
result, we can estimate the temperature interval where the phase transition in
a field ought to lie, if it exists. Although this would-be critical regime is
unreachable with present resources, the numerical challenge is finally well
posed.Comment: 42 pages, 19 figures. Minor changes and added figure (results
unchanged
Embelin binds to human neuroserpin and impairs its polymerisation
Neuroserpin (NS) is a serpin inhibitor of tissue plasminogen activator (tPA) in the brain. The polymerisation of NS pathologic mutants is responsible for a genetic dementia known as familial encephalopathy with neuroserpin inclusion bodies (FENIB). So far, a pharmacological treatment of FENIB, i.e. an inhibitor of NS polymerisation, remains an unmet challenge. Here, we present a biophysical characterisation of the effects caused by embelin (EMB a small natural compound) on NS conformers and NS polymerisation. EMB destabilises all known NS conformers, specifically binding to NS molecules with a 1:1 NS:EMB molar ratio without unfolding the NS fold. In particular, NS polymers disaggregate in the presence of EMB, and their formation is prevented. The NS/EMB complex does not inhibit tPA proteolytic activity. Both effects are pharmacologically relevant: firstly by inhibiting the NS polymerisation associated to FENIB, and secondly by potentially antagonizing metastatic processes facilitated by NS activity in the brain
The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions
Abstract
Background
Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms.
Results
We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation.
Conclusions
Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes.
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