3 research outputs found
A Statistical Modeling Approach to Computer-Aided Quantification of Dental Biofilm
Biofilm is a formation of microbial material on tooth substrata. Several
methods to quantify dental biofilm coverage have recently been reported in the
literature, but at best they provide a semi-automated approach to
quantification with significant input from a human grader that comes with the
graders bias of what are foreground, background, biofilm, and tooth.
Additionally, human assessment indices limit the resolution of the
quantification scale; most commercial scales use five levels of quantification
for biofilm coverage (0%, 25%, 50%, 75%, and 100%). On the other hand, current
state-of-the-art techniques in automatic plaque quantification fail to make
their way into practical applications owing to their inability to incorporate
human input to handle misclassifications. This paper proposes a new interactive
method for biofilm quantification in Quantitative light-induced fluorescence
(QLF) images of canine teeth that is independent of the perceptual bias of the
grader. The method partitions a QLF image into segments of uniform texture and
intensity called superpixels; every superpixel is statistically modeled as a
realization of a single 2D Gaussian Markov random field (GMRF) whose parameters
are estimated; the superpixel is then assigned to one of three classes
(background, biofilm, tooth substratum) based on the training set of data. The
quantification results show a high degree of consistency and precision. At the
same time, the proposed method gives pathologists full control to post-process
the automatic quantification by flipping misclassified superpixels to a
different state (background, tooth, biofilm) with a single click, providing
greater usability than simply marking the boundaries of biofilm and tooth as
done by current state-of-the-art methods.Comment: 10 pages, 7 figures, Journal of Biomedical and Health Informatics
2014. keywords: {Biomedical imaging;Calibration;Dentistry;Estimation;Image
segmentation;Manuals;Teeth},
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6758338&isnumber=636350
BiofilmQuant: A Computer-Assisted Tool for Dental Biofilm Quantification
Dental biofilm is the deposition of microbial material over a tooth
substratum. Several methods have recently been reported in the literature for
biofilm quantification; however, at best they provide a barely automated
solution requiring significant input needed from the human expert. On the
contrary, state-of-the-art automatic biofilm methods fail to make their way
into clinical practice because of the lack of effective mechanism to
incorporate human input to handle praxis or misclassified regions. Manual
delineation, the current gold standard, is time consuming and subject to expert
bias. In this paper, we introduce a new semi-automated software tool,
BiofilmQuant, for dental biofilm quantification in quantitative light-induced
fluorescence (QLF) images. The software uses a robust statistical modeling
approach to automatically segment the QLF image into three classes (background,
biofilm, and tooth substratum) based on the training data. This initial
segmentation has shown a high degree of consistency and precision on more than
200 test QLF dental scans. Further, the proposed software provides the
clinicians full control to fix any misclassified areas using a single click. In
addition, BiofilmQuant also provides a complete solution for the longitudinal
quantitative analysis of biofilm of the full set of teeth, providing greater
ease of usability.Comment: 4 pages, 4 figures, 36th Annual International Conference of the IEEE
Engineering in Medicine and Biology Society (EMBC 2014
Determination of the trajectory of linker DNA by fluorescence energy transfer distance measurements
We have used fluorescence energy transfer distance measurements to study the trajectory of linker DNA as it enters and exits the histone octamer in a nucleosome core particle. Measurement of the DNA-to-protein distances gives important structural information about the most fundamental level of chromosomal organization, and allows speculation about higher order compaction.The implementation of this method required the reconstitution of a nucleosome core particle from natural and synthetic component molecules. The histone octamers are extracted and purified from chicken erythrocytes, specifically labeled with a fluorescent dye (one of a fluorescent energy transfer pair) and further purified. The DNA is produced using polymerase chain reaction (PCR) with fluorescently labeled and HPLC the purified synthetic primers, with template DNA that is extracted, cleaved with restriction enzymes, and HPLC purified from source DNA cloned into E. coli. This template DNA is the 256bp phasing sequence from the 5S RNA gene of Lytechinus variegatus, which allows reconstitution of phased nucleosome core particles. After reconstitution, characterization included fluorescence energy transfer distance measurements as well as HPLC, sedimentation, and enzymatic digests to insure structural integrity.The distance between the protein and a linker DNA end is related to the distance between the attached dye molecules and can be determined by measurement of the energy transfer between this pair. Fluorescence lifetime, anisotropy, and quantum yield measurements are used to determine the magnitude of this transfer, which is proportional to the inverse 1/6\sp{\rm th} power of the distance. These measurements, made as a function of the linker DNA length, indicate the linker DNA entrance and exit trajectory and directly relates to the global architecture of the initial steps in the condensation of a chromosome.U of I OnlyETDs are only available to UIUC Users without author permissio