scholarly journals Novel algorithms for PFGE bacterial typing: Number of co-migrated DNA fragments, linking PFGE to WGS results and computer simulations for evaluation of PulseNet international typing protocols

2020 ◽  
Author(s):  
Ibrahim-Elkhalil M. Adam ◽  
Isam Abdokashif ◽  
Asia Elrashid ◽  
Hiba Bayoumi ◽  
Ahmed Musa ◽  
...  
Keyword(s):  
Image Analysis ◽  
In Silico ◽  
Pathogenic Bacteria ◽  
Restriction Enzymes ◽  
Dna Fragments ◽  
Evaluation Tool ◽  
Bacterial Typing ◽  
Analysis Algorithm ◽  
Image Analysis Algorithm ◽  
Pfge Profiles

AbstractBackgroundStandard protocols for Pulsed-field gel electrophoresis (PFGE) were adopted and being used in a global scale for surveillance of many bacterial food-borne diseases. Matched PFGE bands are considered regardless of co-migration of different DNA fragments. Molecular epidemiology is turning toward whole genome sequencing (WGS). Although, WGS results can be digested In-silico, PFGE and WGS data are being compared separately. We describe a new image analysis algorithm that enables identification of how many DNA fragments co-migrate during PFGE. We built a database that compare described PFGE results to in-silico obtained digestion models (from WGS). Reliability of the method was assessed in-silico using novel computer simulation approach. From WGS, 1,816 digestion model (DMs) were obtained as recommended by PulseNet international. Simulation codes were designed to predict PFGE profiles when DMs are separated at 5% PFGE resolution in addition to expected co-migration levels.ResultsPFGE simulation has shown that about 35% of DNA fragments co-migrate at 5% PFGE resolution. Similar result was obtained when wet-lab PFGE profiles were analyzed using image analysis algorithm mentioned earlier. When image analysis results were compared to DMs, results returned by geltowgs.uofk.edu database revealed reasonable relatedness to DMs. In terms of number of PFGE typable DNA fragments, 45,517 were typable (representing 46.54% out of 97,801). Previously mentioned typable fragments (in terms of typable sizes) comprised 91.24% of the sum of nucleotides of all chromosomes tested (7.24 billion bp). However, significant variations were shown within and between different digestion protocols.ConclusionsIdentification of co-migration levels will reveal the third dimension of PFGE profiles. This will provide a better way for evaluating isolate relationships. Linking old PFGE results to WGS by means of simulation demonstrated here will provide a chance to link millions of PFGE epidemiological data accumulated during the last 24 years to the new WGS era. Evaluation of population dynamics of pathogenic bacteria will be deeper through space and time. Selection of restriction enzymes for PFGE typing will have a powerful in-silico evaluation tool.

scholarly journals PulseNet international: the missing link between PFGE and WGS

2021 ◽  
Author(s):  
Ibrahim-Elkhalil M. Adam
Keyword(s):  
Image Analysis ◽  
Salmonella Enterica ◽  
Evaluation Criteria ◽  
Test Subject ◽  
Data Sets ◽  
Surveillance Network ◽  
Analysis Algorithm ◽  
E Coli ◽  
Image Analysis Algorithm ◽  
Pfge Profiles

AbstractIntroductionDNA-based surveillance of bacterial diseases has been using pulsed field gel electrophoresis (PFGE) since 1996. Currently, the international surveillance network (PulseNet international) is turning toward whole genome sequencing (WGS). ATCGs of WGS are compared using several sequence alignment methods. While patterns of horizontal lines of PFGE profiles are being compared using relative positioning of bands within a range of tolerance. A recently suggested image analysis algorithm and a deployed database (geltowgs.uofk.edu) collectively invented a promising method for comparing PFGE to in-silico obtained digestion models (DMs) derived from WGS. The database requires a parameter that determines PFGE resolution. Here, the author suggests a new method for calculating this factor. Epidemiological and molecular conclusions returned by the database are evaluated.Methodologytwo PFGE profiles representing XbaI digests of E. coli and Salmonella enterica analyzed by the suggested image analysis algorithm were submitted to the database after calculating resolution of PFGE using Dice percentage of difference between the closest PFGE bands in length. E. coli and Salmonella enterica test subjects were compared to 489 and 401 DMs respectively. The three data sets returned were analyzed.Results and conclusionsaccording to modified PFGE evaluation criteria; a single DM is possibly related to E. coli test subject. It belonged to the same serovar. No epidemiologically related DM was shown for S. enterica test subject. Conclusions mentioned earlier could never be made ignoring co-migration. Standardization of both; suggested image analysis and database algorithms will deepen our understanding of bacterial epidemiology by means of possible qualitative approach built upon identification of fragment sequences and their locations within chromosomes.

scholarly journals Analysis algorithm for sky type and ice halo recognition in all-sky images

2019 ◽  
Vol 12 (8) ◽  
pp. 4241-4259 ◽  
Author(s):  
Sylke Boyd ◽  
Stephen Sorenson ◽  
Shelby Richard ◽  
Michelle King ◽  
Morton Greenslit
Keyword(s):  
Time Series ◽  
Image Analysis ◽  
Great Plains ◽  
Detailed Comparison ◽  
Analysis Algorithm ◽  
Long Time Series ◽  
Image Analysis Algorithm ◽  
Long Time ◽  
Atmospheric Radiation Measurement ◽  
Sky Type

Abstract. Halo displays, in particular the 22∘ halo, have been captured in long time series of images obtained from total sky imagers (TSIs) at various Atmospheric Radiation Measurement (ARM) sites. Halo displays form if smooth-faced hexagonal ice crystals are present in the optical path. We describe an image analysis algorithm for long time series of TSI images which scores images with respect to the presence of 22∘ halos. Each image is assigned an ice halo score (IHS) for 22∘ halos, as well as a photographic sky type (PST), which differentiates cirrostratus (PST-CS), partially cloudy (PST-PCL), cloudy (PST-CLD), or clear (PST-CLR) within a near-solar image analysis area. The color-resolved radial brightness behavior of the near-solar region is used to define the discriminant properties used to classify photographic sky type and assign an ice halo score. The scoring is based on the tools of multivariate Gaussian analysis applied to a standardized sun-centered image produced from the raw TSI image, following a series of calibrations, rotation, and coordinate transformation. The algorithm is trained based on a training set for each class of images. We present test results on halo observations and photographic sky type for the first 4 months of the year 2018, for TSI images obtained at the Southern Great Plains (SGP) ARM site. A detailed comparison of visual and algorithm scores for the month of March 2018 shows that the algorithm is about 90 % reliable in discriminating the four photographic sky types and identifies 86 % of all visual halos correctly. Numerous instances of halo appearances were identified for the period January through April 2018, with persistence times between 5 and 220 min. Varying by month, we found that between 9 % and 22 % of cirrostratus skies exhibited a full or partial 22∘ halo.

scholarly journals Osteoid Metaplasia in Femoral Artery Plaques Is Associated With the Clinical Severity of Lower Extremity Artery Disease in Men

2020 ◽  
Vol 7 ◽  
Author(s):  
Mirjami Laivuori ◽  
Johanna Tolva ◽  
A. Inkeri Lokki ◽  
Nina Linder ◽  
Johan Lundin ◽  
...  
Keyword(s):  
Image Analysis ◽  
Deep Learning ◽  
Lower Extremity ◽  
Femoral Artery ◽  
Analysis Algorithm ◽  
Image Analysis Algorithm ◽  
Artery Disease ◽  
Area Percentage ◽  
Lower Extremity Artery Disease ◽  
Whole Slide Images

Lamellar metaplastic bone, osteoid metaplasia (OM), is found in atherosclerotic plaques, especially in the femoral arteries. In the carotid arteries, OM has been documented to be associated with plaque stability. This study investigated the clinical impact of OM load in femoral artery plaques of patients with lower extremity artery disease (LEAD) by using a deep learning-based image analysis algorithm. Plaques from 90 patients undergoing endarterectomy of the common femoral artery were collected and analyzed. After decalcification and fixation, 4-μm-thick longitudinal sections were stained with hematoxylin and eosin, digitized, and uploaded as whole-slide images on a cloud-based platform. A deep learning-based image analysis algorithm was trained to analyze the area percentage of OM in whole-slide images. Clinical data were extracted from electronic patient records, and the association with OM was analyzed. Fifty-one (56.7%) sections had OM. Females with diabetes had a higher area percentage of OM than females without diabetes. In male patients, the area percentage of OM inversely correlated with toe pressure and was significantly associated with severe symptoms of LEAD including rest pain, ulcer, or gangrene. According to our results, OM is a typical feature of femoral artery plaques and can be quantified using a deep learning-based image analysis method. The association of OM load with clinical features of LEAD appears to differ between male and female patients, highlighting the need for a gender-specific approach in the study of the mechanisms of atherosclerotic disease. In addition, the role of plaque characteristics in the treatment of atherosclerotic lesions warrants further consideration in the future.

scholarly journals Validation of an image analysis algorithm to quantify leukocyte populations using whole slide image analysis

2013 ◽  
Vol 1 (S1) ◽  
Author(s):  
Anthony J Milici ◽  
David Young ◽  
Steven J Potts ◽  
Holger Lange ◽  
Nicholas D Landis ◽  
...  
Keyword(s):  
Image Analysis ◽  
Analysis Algorithm ◽  
Whole Slide Image ◽  
Image Analysis Algorithm ◽  
Slide Image ◽  
Leukocyte Populations
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