44 research outputs found
Statistically Adaptive Filtering for Low Signal Correction in X-ray Computed Tomography
Low x-ray dose is desirable in x-ray computed tomographic (CT) imaging due to
health concerns. But low dose comes with a cost of low signal artifacts such as
streaks and low frequency bias in the reconstruction. As a result, low signal
correction is needed to help reduce artifacts while retaining relevant
anatomical structures.
Low signal can be encountered in cases where sufficient number of photons do
not reach the detector to have confidence in the recorded data. % NOTE: SNR is
ratio of powers, not std. dev. X-ray photons, assumed to have Poisson
distribution, have signal to noise ratio proportional to the dose, with poorer
SNR in low signal areas. Electronic noise added by the data acquisition system
further reduces the signal quality.
In this paper we will demonstrate a technique to combat low signal artifacts
through adaptive filtration. It entails statistics-based filtering on the
uncorrected data, correcting the lower signal areas more aggressively than the
high signal ones. We look at local averages to decide how aggressive the
filtering should be, and local standard deviation to decide how much detail
preservation to apply. Implementation consists of a pre-correction step i.e.
local linear minimum mean-squared error correction, followed by a variance
stabilizing transform, and finally adaptive bilateral filtering. The
coefficients of the bilateral filter are computed using local statistics.
Results show that improvements were made in terms of low frequency bias,
streaks, local average and standard deviation, modulation transfer function and
noise power spectrum
MBIR Training for a 2.5D DL network in X-ray CT
In computed tomographic imaging, model based iterative reconstruction methods
have generally shown better image quality than the more traditional, faster
filtered backprojection technique. The cost we have to pay is that MBIR is
computationally expensive. In this work we train a 2.5D deep learning (DL)
network to mimic MBIR quality image. The network is realized by a modified
Unet, and trained using clinical FBP and MBIR image pairs. We achieve the
quality of MBIR images faster and with a much smaller computation cost.
Visually and in terms of noise power spectrum (NPS), DL-MBIR images have
texture similar to that of MBIR, with reduced noise power. Image profile plots,
NPS plots, standard deviation, etc. suggest that the DL-MBIR images result from
a successful emulation of an MBIR operator
Design of Novel Loss Functions for Deep Learning in X-ray CT
Deep learning (DL) shows promise of advantages over conventional signal
processing techniques in a variety of imaging applications. The networks' being
trained from examples of data rather than explicitly designed allows them to
learn signal and noise characteristics to most effectively construct a mapping
from corrupted data to higher quality representations. In inverse problems, one
has options of applying DL in the domain of the originally captured data, in
the transformed domain of the desired final representation, or both.
X-ray computed tomography (CT), one of the most valuable tools in medical
diagnostics, is already being improved by DL methods. Whether for removal of
common quantum noise resulting from the Poisson-distributed photon counts, or
for reduction of the ill effects of metal implants on image quality,
researchers have begun employing DL widely in CT. The selection of training
data is driven quite directly by the corruption on which the focus lies.
However, the way in which differences between the target signal and measured
data is penalized in training generally follows conventional, pointwise loss
functions.
This work introduces a creative technique for favoring reconstruction
characteristics that are not well described by norms such as mean-squared or
mean-absolute error. Particularly in a field such as X-ray CT, where
radiologists' subjective preferences in image characteristics are key to
acceptance, it may be desirable to penalize differences in DL more creatively.
This penalty may be applied in the data domain, here the CT sinogram, or in the
reconstructed image. We design loss functions for both shaping and selectively
preserving frequency content of the signal
Dimerization of the transmembrane domain of amyloid precursor proteins and familial Alzheimer's disease mutants
<p>Abstract</p> <p>Background</p> <p>Amyloid precursor protein (APP) is enzymatically cleaved by γ-secretase to form two peptide products, either Aβ40 or the more neurotoxic Aβ42. The Aβ42/40 ratio is increased in many cases of familial Alzheimer's disease (FAD). The transmembrane domain (TM) of APP contains the known dimerization motif GXXXA. We have investigated the dimerization of both wild type and FAD mutant APP transmembrane domains.</p> <p>Results</p> <p>Using synthetic peptides derived from the APP-TM domain, we show that this segment is capable of forming stable transmembrane dimers. A model of a dimeric APP-TM domain reveals a putative dimerization interface, and interestingly, majority of FAD mutations in APP are localized to this interface region. We find that FAD-APP mutations destabilize the APP-TM dimer and increase the population of APP peptide monomers.</p> <p>Conclusion</p> <p>The dissociation constants are correlated to both the Aβ42/Aβ40 ratio and the mean age of disease onset in AD patients. We also show that these TM-peptides reduce Aβ production and Aβ42/Aβ40 ratios when added to HEK293 cells overexpressing the Swedish FAD mutation and γ-secretase components, potentially revealing a new class of γ-secretase inhibitors.</p
The glucosyltransferase activity of C. difficile toxin b is required for disease pathogenesis
© 2020 Bilverstone et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Enzymatic inactivation of Rho-family GTPases by the glucosyltransferase domain of Clostridioides difficile Toxin B (TcdB) gives rise to various pathogenic effects in cells that are classically thought to be responsible for the disease symptoms associated with C. difficile infection (CDI). Recent in vitro studies have shown that TcdB can, under certain circumstances, induce cellular toxicities that are independent of glucosyltransferase (GT) activity, calling into question the precise role of GT activity. Here, to establish the importance of GT activity in CDI disease pathogenesis, we generated the first described mutant strain of C. difficile producing glucosyltransferase-defective (GT-defective) toxin. Using allelic exchange (AE) technology, we first deleted tcdA in C. difficile 630Δerm and subsequently introduced a deactivating D270N substitution in the GT domain of TcdB. To examine the role of GT activity in vivo, we tested each strain in two different animal models of CDI pathogenesis. In the non-lethal murine model of infection, the GT-defective mutant induced minimal pathology in host tissues as compared to the profound caecal inflammation seen in the wild-type and 630ΔermΔtcdA (ΔtcdA) strains. In the more sensitive hamster model of CDI, whereas hamsters in the wild-type or ΔtcdA groups succumbed to fulminant infection within 4 days, all hamsters infected with the GT-defective mutant survived the 10-day infection period without primary symptoms of CDI or evidence of caecal inflammation. These data demonstrate that GT activity is indispensable for disease pathogenesis and reaffirm its central role in disease and its importance as a therapeutic target for small-molecule inhibition
Environmental pleiotropy and demographic history direct adaptation under antibiotic selection
Evolutionary rescue following environmental change requires mutations permitting population growth in the new environment. If change is severe enough to prevent most of the population reproducing, rescue becomes reliant on mutations already present. If change is sustained, the fitness effects in both environments, and how they are associated-termed 'environmental pleiotropy'-may determine which alleles are ultimately favoured. A population's demographic history-its size over time-influences the variation present. Although demographic history is known to affect the probability of evolutionary rescue, how it interacts with environmental pleiotropy during severe and sustained environmental change remains unexplored. Here, we demonstrate how these factors interact during antibiotic resistance evolution, a key example of evolutionary rescue fuelled by pre-existing mutations with pleiotropic fitness effects. We combine published data with novel simulations to characterise environmental pleiotropy and its effects on resistance evolution under different demographic histories. Comparisons among resistance alleles typically revealed no correlation for fitness-i.e., neutral pleiotropy-above and below the sensitive strain's minimum inhibitory concentration. Resistance allele frequency following experimental evolution showed opposing correlations with their fitness effects in the presence and absence of antibiotic. Simulations demonstrated that effects of environmental pleiotropy on allele frequencies depended on demographic history. At the population level, the major influence of environmental pleiotropy was on mean fitness, rather than the probability of evolutionary rescue or diversity. Our work suggests that determining both environmental pleiotropy and demographic history is critical for predicting resistance evolution, and we discuss the practicalities of this during in vivo evolution
Iron Behaving Badly: Inappropriate Iron Chelation as a Major Contributor to the Aetiology of Vascular and Other Progressive Inflammatory and Degenerative Diseases
The production of peroxide and superoxide is an inevitable consequence of
aerobic metabolism, and while these particular "reactive oxygen species" (ROSs)
can exhibit a number of biological effects, they are not of themselves
excessively reactive and thus they are not especially damaging at physiological
concentrations. However, their reactions with poorly liganded iron species can
lead to the catalytic production of the very reactive and dangerous hydroxyl
radical, which is exceptionally damaging, and a major cause of chronic
inflammation. We review the considerable and wide-ranging evidence for the
involvement of this combination of (su)peroxide and poorly liganded iron in a
large number of physiological and indeed pathological processes and
inflammatory disorders, especially those involving the progressive degradation
of cellular and organismal performance. These diseases share a great many
similarities and thus might be considered to have a common cause (i.e.
iron-catalysed free radical and especially hydroxyl radical generation). The
studies reviewed include those focused on a series of cardiovascular, metabolic
and neurological diseases, where iron can be found at the sites of plaques and
lesions, as well as studies showing the significance of iron to aging and
longevity. The effective chelation of iron by natural or synthetic ligands is
thus of major physiological (and potentially therapeutic) importance. As
systems properties, we need to recognise that physiological observables have
multiple molecular causes, and studying them in isolation leads to inconsistent
patterns of apparent causality when it is the simultaneous combination of
multiple factors that is responsible. This explains, for instance, the
decidedly mixed effects of antioxidants that have been observed, etc...Comment: 159 pages, including 9 Figs and 2184 reference