4,492 research outputs found
Handling oversampling in dynamic networks using link prediction
Oversampling is a common characteristic of data representing dynamic
networks. It introduces noise into representations of dynamic networks, but
there has been little work so far to compensate for it. Oversampling can affect
the quality of many important algorithmic problems on dynamic networks,
including link prediction. Link prediction seeks to predict edges that will be
added to the network given previous snapshots. We show that not only does
oversampling affect the quality of link prediction, but that we can use link
prediction to recover from the effects of oversampling. We also introduce a
novel generative model of noise in dynamic networks that represents
oversampling. We demonstrate the results of our approach on both synthetic and
real-world data.Comment: ECML/PKDD 201
Determining Principal Component Cardinality through the Principle of Minimum Description Length
PCA (Principal Component Analysis) and its variants areubiquitous techniques
for matrix dimension reduction and reduced-dimensionlatent-factor extraction.
One significant challenge in using PCA, is thechoice of the number of principal
components. The information-theoreticMDL (Minimum Description Length) principle
gives objective compression-based criteria for model selection, but it is
difficult to analytically applyits modern definition - NML (Normalized Maximum
Likelihood) - to theproblem of PCA. This work shows a general reduction of NML
prob-lems to lower-dimension problems. Applying this reduction, it boundsthe
NML of PCA, by terms of the NML of linear regression, which areknown.Comment: LOD 201
Positive Semidefiniteness and Positive Definiteness of a Linear Parametric Interval Matrix
We consider a symmetric matrix, the entries of which depend linearly on some
parameters. The domains of the parameters are compact real intervals. We
investigate the problem of checking whether for each (or some) setting of the
parameters, the matrix is positive definite (or positive semidefinite). We
state a characterization in the form of equivalent conditions, and also propose
some computationally cheap sufficient\,/\,necessary conditions. Our results
extend the classical results on positive (semi-)definiteness of interval
matrices. They may be useful for checking convexity or non-convexity in global
optimization methods based on branch and bound framework and using interval
techniques
Brain immune cells undergo cGAS-STING-dependent apoptosis during herpes simplex virus type 1 infection
Protection of the brain from viral infections involves the type I interferon (IFN-I) system, defects in which renders humans susceptible to herpes simplex encephalitis (HSE). However, excessive cerebral IFN-I levels leads to pathologies, suggesting the need for tight regulation of responses. Based on data from mouse models, human HSE cases, and primary cell culture systems, we here show that microglia and other immune cells undergo apoptosis in the HSV-1-infected brain through a mechanism dependent on the cyclic GMP-AMP synthase (cGAS) - stimulator of interferon genes (STING) pathway, but independent of IFN-I. HSV-1 infection of microglia induced cGAS-dependent apoptosis at high viral doses, while lower viral doses led to IFN-I responses. Importantly, inhibition of caspase activity prevented microglial cell death and augmented IFN-I responses. Accordingly, HSV-1-infected organotypic brain slices, or mice treated with caspase inhibitor, exhibited lower viral load and improved outcome of infection. Collectively, we identify an activation-induced apoptosis program in brain immune cells which down-modulates local immune responses
Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4
The small ubiquitin-like modifier (SUMO) can form polymeric chains that are important signals in cellular processes such as meiosis, genome maintenance and stress response. The SUMO-targeted ubiquitin ligase RNF4 engages with SUMO chains on linked substrates and catalyses their ubiquitination, which targets substrates for proteasomal degradation. Here we use a segmental labelling approach combined with solution nuclear magnetic resonance (NMR) spectroscopy and biochemical characterization to reveal how RNF4 manipulates the conformation of the SUMO chain, thereby facilitating optimal delivery of the distal SUMO domain for ubiquitin transfer
Extending colonic mucosal microbiome analysis - Assessment of colonic lavage as a proxy for endoscopic colonic biopsies
This study was supported through GI Research funds and MRC Grant Ref: MR/M00533X/1 to GH.Peer reviewedPublisher PD
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