1,068 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
A biophysical model of prokaryotic diversity in geothermal hot springs
Recent field investigations of photosynthetic bacteria living in geothermal
hot spring environments have revealed surprisingly complex ecosystems, with an
unexpected level of genetic diversity. One case of particular interest involves
the distribution along hot spring thermal gradients of genetically distinct
bacterial strains that differ in their preferred temperatures for reproduction
and photosynthesis. In such systems, a single variable, temperature, defines
the relevant environmental variation. In spite of this, each region along the
thermal gradient exhibits multiple strains of photosynthetic bacteria adapted
to several distinct thermal optima, rather than the expected single thermal
strain adapted to the local environmental temperature. Here we analyze
microbiology data from several ecological studies to show that the thermal
distribution field data exhibit several universal features independent of
location and specific bacterial strain. These include the distribution of
optimal temperatures of different thermal strains and the functional dependence
of the net population density on temperature. Further, we present a simple
population dynamics model of these systems that is highly constrained by
biophysical data and by physical features of the environment. This model can
explain in detail the observed diversity of different strains of the
photosynthetic bacteria. It also reproduces the observed thermal population
distributions, as well as certain features of population dynamics observed in
laboratory studies of the same organisms
Case Report Q Fever with Unusual Exposure History: A Classic Presentation of a Commonly Misdiagnosed Disease
We describe the case of a man presumptively diagnosed and treated for Rocky Mountain spotted fever following exposure to multiple ticks while riding horses. The laboratory testing of acute and convalescent serum specimens led to laboratory confirmation of acute Q fever as the etiology. This case represents a potential tickborne transmission of Coxiella burnetii and highlights the importance of considering Q fever as a possible diagnosis following tick exposures
Hsp90 governs dispersion and drug resistance of fungal biofilms
Fungal biofilms are a major cause of human mortality and are recalcitrant to most treatments due to intrinsic drug resistance. These complex communities of multiple cell types form on indwelling medical devices and their eradication often requires surgical removal of infected devices. Here we implicate the molecular chaperone Hsp90 as a key regulator of biofilm dispersion and drug resistance. We previously established that in the leading human fungal pathogen, Candida albicans, Hsp90 enables the emergence and maintenance of drug resistance in planktonic conditions by stabilizing the protein phosphatase calcineurin and MAPK Mkc1. Hsp90 also regulates temperature-dependent C. albicans morphogenesis through repression of cAMP-PKA signalling. Here we demonstrate that genetic depletion of Hsp90 reduced C. albicans biofilm growth and maturation in vitro and impaired dispersal of biofilm cells. Further, compromising Hsp90 function in vitro abrogated resistance of C. albicans biofilms to the most widely deployed class of antifungal drugs, the azoles. Depletion of Hsp90 led to reduction of calcineurin and Mkc1 in planktonic but not biofilm conditions, suggesting that Hsp90 regulates drug resistance through different mechanisms in these distinct cellular states. Reduction of Hsp90 levels led to a marked decrease in matrix glucan levels, providing a compelling mechanism through which Hsp90 might regulate biofilm azole resistance. Impairment of Hsp90 function genetically or pharmacologically transformed fluconazole from ineffectual to highly effective in eradicating biofilms in a rat venous catheter infection model. Finally, inhibition of Hsp90 reduced resistance of biofilms of the most lethal mould, Aspergillus fumigatus, to the newest class of antifungals to reach the clinic, the echinocandins. Thus, we establish a novel mechanism regulating biofilm drug resistance and dispersion and that targeting Hsp90 provides a much-needed strategy for improving clinical outcome in the treatment of biofilm infections
Identification and Characterization of Antifungal Compounds Using a Saccharomyces cerevisiae Reporter Bioassay
New antifungal drugs are urgently needed due to the currently limited selection, the emergence of drug resistance, and the toxicity of several commonly used drugs. To identify drug leads, we screened small molecules using a Saccharomyces cerevisiae reporter bioassay in which S. cerevisiae heterologously expresses Hik1, a group III hybrid histidine kinase (HHK) from Magnaporthe grisea. Group III HHKs are integral in fungal cell physiology, and highly conserved throughout this kingdom; they are absent in mammals, making them an attractive drug target. Our screen identified compounds 13 and 33, which showed robust activity against numerous fungal genera including Candida spp., Cryptococcus spp. and molds such as Aspergillus fumigatus and Rhizopus oryzae. Drug-resistant Candida albicans from patients were also highly susceptible to compounds 13 and 33. While the compounds do not act directly on HHKs, microarray analysis showed that compound 13 induced transcripts associated with oxidative stress, and compound 33, transcripts linked with heavy metal stress. Both compounds were highly active against C. albicans biofilm, in vitro and in vivo, and exerted synergy with fluconazole, which was inactive alone. Thus, we identified potent, broad-spectrum antifungal drug leads from a small molecule screen using a high-throughput, S. cerevisiae reporter bioassay
Draft Genome Sequence of the Marine Streptomyces sp. Strain PP-C42, Isolated from the Baltic Sea
Streptomyces, a branch of aerobic Gram-positive bacteria represents the largest genus of actinobacteria. The streptomycetes are characterized by a complex secondary metabolism and produce over two-thirds of the clinically used natural antibiotics today. Here we report the draft genome sequence of a Streptomyces strain PP-C42 isolated from the marine environment. A subset of unique genes and gene clusters for diverse secondary metabolites as well as antimicrobial peptides (AMPs) could be identified from the genome, showing great promise as a source for novel bioactive compound
Draft Genome Sequence of the Marine Streptomyces sp. Strain PP-C42, Isolated from the Baltic Sea
Streptomyces, a branch of aerobic Gram-positive bacteria represents the largest genus of actinobacteria. The streptomycetes are characterized by a complex secondary metabolism and produce over two-thirds of the clinically used natural antibiotics today. Here we report the draft genome sequence of a Streptomyces strain PP-C42 isolated from the marine environment. A subset of unique genes and gene clusters for diverse secondary metabolites as well as antimicrobial peptides (AMPs) could be identified from the genome, showing great promise as a source for novel bioactive compound
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