3,226 research outputs found
Classification of interstitial lung disease patterns with topological texture features
Topological texture features were compared in their ability to classify
morphological patterns known as 'honeycombing' that are considered indicative
for the presence of fibrotic interstitial lung diseases in high-resolution
computed tomography (HRCT) images. For 14 patients with known occurrence of
honey-combing, a stack of 70 axial, lung kernel reconstructed images were
acquired from HRCT chest exams. A set of 241 regions of interest of both
healthy and pathological (89) lung tissue were identified by an experienced
radiologist. Texture features were extracted using six properties calculated
from gray-level co-occurrence matrices (GLCM), Minkowski Dimensions (MDs), and
three Minkowski Functionals (MFs, e.g. MF.euler). A k-nearest-neighbor (k-NN)
classifier and a Multilayer Radial Basis Functions Network (RBFN) were
optimized in a 10-fold cross-validation for each texture vector, and the
classification accuracy was calculated on independent test sets as a
quantitative measure of automated tissue characterization. A Wilcoxon
signed-rank test was used to compare two accuracy distributions and the
significance thresholds were adjusted for multiple comparisons by the
Bonferroni correction. The best classification results were obtained by the MF
features, which performed significantly better than all the standard GLCM and
MD features (p < 0.005) for both classifiers. The highest accuracy was found
for MF.euler (97.5%, 96.6%; for the k-NN and RBFN classifier, respectively).
The best standard texture features were the GLCM features 'homogeneity' (91.8%,
87.2%) and 'absolute value' (90.2%, 88.5%). The results indicate that advanced
topological texture features can provide superior classification performance in
computer-assisted diagnosis of interstitial lung diseases when compared to
standard texture analysis methods.Comment: 8 pages, 5 figures, Proceedings SPIE Medical Imaging 201
Minimizing the effect of sinusoidal trends in detrended fluctuation analysis
The detrended fluctuation analysis (DFA) [Peng et al., 1994] and its
extensions (MF-DFA) [Kantelhardt et al., 2002] have been used extensively to
determine possible long-range correlations in self-affine signals. While the
DFA has been claimed to be a superior technique, recent reports have indicated
its susceptibility to trends in the data. In this report, a smoothing filter is
proposed to minimize the effect of sinusoidal trends and distortion in the
log-log plots obtained by DFA and MF-DFA techniques
Phase Coexistence Near a Morphotropic Phase Boundary in Sm-doped BiFeO3 Films
We have investigated heteroepitaxial films of Sm-doped BiFeO3 with a
Sm-concentration near a morphotropic phase boundary. Our high-resolution
synchrotron X-ray diffraction, carried out in a temperature range of 25C to
700C, reveals substantial phase coexistence as one changes temperature to
crossover from a low-temperature PbZrO3-like phase to a high-temperature
orthorhombic phase. We also examine changes due to strain for films greater or
less than the critical thickness for misfit dislocation formation.
Particularly, we note that thicker films exhibit a substantial volume collapse
associated with the structural transition that is suppressed in strained thin
films
Estimating scenarios for domestic water demand under drought conditions in England and Wales
This paper presents preliminary results from the development of IMPETUS model, a domestic water demand microsimulation model which was developed to estimate the results of a range of scenarios of domestic demand under drought conditions. The model is intended to enable water resource management practitioners to assess the likely impact of potential interventions in particular catchment areas. It has been designed to be driven by seasonal catchment level forecasts of potential hydrological droughts based on innovative climate and groundwater models. The current version of the model is driven by reconstructed historical drought data for the Colne catchment in the East of England from 1995 to 2014. This provides a framework of five drought phases (Normal, Developing, Drought, Severe and Recovering) which are mapped to policy driven interventions such as increased provision of water efficiency technologies and temporary water-use bans. The model uses UK Census 2011 data to develop a synthetic household population that matches the socio-demographics of the catchment and it microsimulates (at the household level) the consequences of water efficiency interventions retrospectively (1995-2014). Demand estimates for reconstructed drought histories are presented to demonstrate the potential value of the model in supporting cost-benefit analysis of specific interventions. We conclude by discussing future directions for the work
Reflection confocal nanoscopy using a super-oscillatory lens
A Superoscillatory lens (SOL) is known to produce a sub-diffraction hotspot
which is useful for high-resolution imaging. However, high-energy rings called
sidelobes coexist with the central hotspot. Additionally, SOLs have not yet
been directly used to image reflective objects due to low efficiency and poor
imaging properties. We propose a novel reflection confocal nanoscope which
mitigates these issues by relaying the SOL intensity pattern onto the object
and use conventional optics for detection. We experimentally demonstrate
super-resolution by imaging double bars with 330 nm separation using a 632.8 nm
excitation and a 0.95 NA objective. We also discuss the enhanced contrast
properties of the SOL nanoscope against a laser confocal microscope, and the
degradation of performance while imaging large objects.Comment: 17 pages, 15 figures, supplementary include
Adenoviral oncoprotein E1B55K mediates colocalization of SSBP2 and PML in response to stress
Transient expression of adenoviral oncoprotein E1B55K in normal cells induces aggresome formation and sequestration of critical host proteins in aggresomes. Our previous studies reported that Sequence Specific Binding Protein 2 (SSBP2), a candidate tumor suppressor is recruited to aggresomes in adenovirally transformed human embryonal kidney 293 (HEK293) cells. To understand the extent and significance of the E1B55K-SSBP2 interactions in these cells, we have examined SSBP2 localization under conditions of stress in HEK293 cells. SSBP2 localizes to PML- Nuclear Bodies (PML-NBs) in response to inhibition of nuclear export, treatment with etoposide, hydroxyurea or gamma irradiation only in HEK293 cells. Furthermore, the PML-NBs grow in size and number in response to radiation over a 24 hour period in HEK293 cells analogous to previous findings for other cell types. Nonetheless, we conclude that E1B55K subverts SSBP2 function in HEK293 cells. These findings demonstrate the limitations in using HEK293 cells to study DNA damage response and other cellular processes since SSBP2 and similar regulatory proteins are aberrantly localized due to constitutive E1B55K expression
Cis-activation in the Notch signaling pathway
The Notch signaling pathway consists of transmembrane ligands and receptors that can interact both within the same cell (cis) and across cell boundaries (trans). Previous work has shown that cis-interactions act to inhibit productive signaling. Here, by analyzing Notch activation in single cells while controlling cell density and ligand expression level, we show that cis-ligands can also activate Notch receptors. This cis-activation process resembles trans-activation in its ligand level dependence, susceptibility to cis-inhibition, and sensitivity to Fringe modification. Cis-activation occurred for multiple ligand-receptor pairs, in diverse cell types, and affected survival in neural stem cells. Finally, mathematical modeling shows how cis-activation could potentially expand the capabilities of Notch signaling, for example enabling ‘negative’ (repressive) signaling. These results establish cis-activation as an additional mode of signaling in the Notch pathway, and should contribute to a more complete understanding of how Notch signaling functions in developmental, physiological, and biomedical contexts
An operational view of intercellular signaling pathways
Animal cells use a conserved repertoire of intercellular signaling pathways to communicate with one another. These pathways are well-studied from a molecular point of view. However, we often lack an “operational” understanding that would allow us to use these pathways to rationally control cellular behaviors. This requires knowing what dynamic input features each pathway perceives and how it processes those inputs to control downstream processes. To address these questions, researchers have begun to reconstitute signaling pathways in living cells, analyzing their dynamic responses to stimuli, and developing new functional representations of their behavior. Here we review important insights obtained through these new approaches, and discuss challenges and opportunities in understanding signaling pathways from an operational point of view
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