scholarly journals Erratum: Pixel-Based Machine Learning and Image Reconstitution for Dot-ELISA Pathogen Diagnosis in Biological Samples

2021 ◽  
Vol 12 ◽  
Author(s):  
The Analyst ◽  
2021 ◽  
Author(s):  
Nicolas Pavillon ◽  
Nicholas I Smith

Raman spectroscopy has the ability to retrieve molecular information from live biological samples non-invasively through optical means. Coupled with machine learning, it is possible to use this large amount of...


2020 ◽  
Vol 38 ◽  
pp. 76-82
Author(s):  
Yusuke Ono ◽  
Tsutomu Matsuura ◽  
Toshiyuki Matsuzaki ◽  
Keiju Hiromura ◽  
Takeo Aoki

In general, we need a lot of data for improving the accuracy of machine learning. However, the number of biological samples what we can obtain are not enough for machine learning. This problem exists in the classification of glomerular epithelial cells with the progress of disease, and its accuracy is contrary to our intuitive impression. Therefore, we would like to improve the accuracy by generating a lot of fake images using Generative Adversarial Nets (GANs). About podocyte cells, it was difficult to obtain an arbitrary disease by previous method. In this paper, we propose the model with restriction of learning by shapes information based on ACGANs, and we investigate how much fake images generated by our method are similar to real images. According to the results, the passage number of fake images by our method is 17% higher than conventional method.


2020 ◽  
Author(s):  
Cleo Anastassopoulou ◽  
Athanasios Tsakris ◽  
George P. Patrinos ◽  
Yiannis Manoussopoulos

AbstractSerological methods serve as a direct or indirect means of pathogen infection diagnosis in plant and animal species, including humans. Dot-ELISA (DE) is an inexpensive and sensitive, solid-state version of the microplate enzyme-linked immunosorbent assay, with a broad range of applications in epidemiology. Yet, its applicability is limited by uncertainties in the qualitative output of the assay due to overlapping dot colorations of positive and negative samples, stemming mainly from the inherent color discrimination thresholds of the human eye. Here, we report a novel approach for unambiguous DE output evaluation by applying machine learning-based pattern recognition of image pixels of the blot using an impartial predictive model rather than human judgment. Supervised machine learning was used to train a classifier algorithm through a built multivariate logistic regression model based on the RGB (“Red”, “Green”, “Blue”) pixel attributes of a scanned DE output of samples of known infection status to a model pathogen (Lettuce big-vein associated virus). Based on the trained and cross-validated algorithm, pixel probabilities of unknown samples could be predicted in scanned DE output images which would then be reconstituted by pixels having probabilities above a cutoff that may be selected at will to yield desirable false positive and false negative rates depending on the question at hand, thus allowing for proper dot classification of positive and negative samples and, hence, accurate diagnosis. Potential improvements and diagnostic applications of the proposed versatile method that translates unique pathogen antigens to the universal basic color language are discussed.


2019 ◽  
Author(s):  
Florence Roux-Dalvai ◽  
Clarisse Gotti ◽  
Mickaël Leclercq ◽  
Marie-Claude Hélie ◽  
Maurice Boissinot ◽  
...  

ABSTRACTThe identification of microbial species in biological samples is essential to many applications in health, food safety and environment. MALDI-TOF MS technology has become a tool of choice for microbial identification but it has several drawbacks including: it requires a long step of bacterial culture prior to analysis (24h), it has a low specificity and is not quantitative. We have developed a new strategy for identifying bacterial species in biological samples using specific LC-MS/MS peptidic signatures. In the first training step, deep proteome coverage of bacteria of interest is obtained in Data Independent Acquisition (DIA) mode, followed by the use of machine learning to define the peptides the most susceptible to distinguish each bacterial species from the others. Then, in the second step, this peptidic signature is monitored in biological samples using targeted proteomics. This method, which allows the bacterial identification from clinical specimens in less than 4h, has been applied to fifteen species representing 84% of all Urinary Tract Infections (UTI). More than 31000 peptides in 200 samples have been quantified by DIA and analyzed by machine learning to determine an 82 peptides signature and build prediction models able to classify the fifteen bacterial species. This peptidic signature was validated for its use in routine conditions using Parallel Reaction Monitoring on a capillary flow chromatography coupled to a Thermo Scientific™ Q Exactive HF-X instrument. Linearity and reproducibility of the method were demonstrated as well as its accuracy on donor specimens. Within 4h and without bacterial culture, our method was able to predict the predominant bacteria infecting a sample in 97% of cases and 100% above the 1×105 CFU/mL threshold commonly used by clinical laboratories. This work demonstrates the efficiency of our method for the rapid and specific identification of the bacterial species causing UTI and could be extended in the future to other biological specimens and to bacteria having specific virulence or resistance factors.


2021 ◽  
Vol 12 ◽  
Author(s):  
Cleo Anastassopoulou ◽  
Athanasios Tsakris ◽  
George P. Patrinos ◽  
Yiannis Manoussopoulos

Serological methods serve as a direct or indirect means of pathogen infection diagnosis in plant and animal species, including humans. Dot-ELISA (DE) is an inexpensive and sensitive, solid-state version of the microplate enzyme-linked immunosorbent assay, with a broad range of applications in epidemiology. Yet, its applicability is limited by uncertainties in the qualitative output of the assay due to overlapping dot colorations of positive and negative samples, stemming mainly from the inherent color discrimination thresholds of the human eye. Here, we report a novel approach for unambiguous DE output evaluation by applying machine learning-based pattern recognition of image pixels of the blot using an impartial predictive model rather than human judgment. Supervised machine learning was used to train a classifier algorithm through a built multivariate logistic regression model based on the RGB (“Red,” “Green,” “Blue”) pixel attributes of a scanned DE output of samples of known infection status to a model pathogen (Lettuce big-vein associated virus). Based on the trained and cross-validated algorithm, pixel probabilities of unknown samples could be predicted in scanned DE output images, which would then be reconstituted by pixels having probabilities above a cutoff. The cutoff may be selected at will to yield desirable false positive and false negative rates depending on the question at hand, thus allowing for proper dot classification of positive and negative samples and, hence, accurate diagnosis. Potential improvements and diagnostic applications of the proposed versatile method that translates unique pathogen antigens to the universal basic color language are discussed.


2020 ◽  
Vol 43 ◽  
Author(s):  
Myrthe Faber

Abstract Gilead et al. state that abstraction supports mental travel, and that mental travel critically relies on abstraction. I propose an important addition to this theoretical framework, namely that mental travel might also support abstraction. Specifically, I argue that spontaneous mental travel (mind wandering), much like data augmentation in machine learning, provides variability in mental content and context necessary for abstraction.


Author(s):  
W. R. Schucany ◽  
G. H. Kelsoe ◽  
V. F. Allison

Accurate estimation of the size of spheroid organelles from thin sectioned material is often necessary, as uniquely homogenous populations of organelles such as vessicles, granules, or nuclei often are critically important in the morphological identification of similar cell types. However, the difficulty in obtaining accurate diameter measurements of thin sectioned organelles is well known. This difficulty is due to the extreme tenuity of the sectioned material as compared to the size of the intact organelle. In populations where low variance is suspected the traditional method of diameter estimation has been to measure literally hundreds of profiles and to describe the “largest” as representative of the “approximate maximal diameter”.


Author(s):  
C. F. Oster

Although ultra-thin sectioning techniques are widely used in the biological sciences, their applications are somewhat less popular but very useful in industrial applications. This presentation will review several specific applications where ultra-thin sectioning techniques have proven invaluable.The preparation of samples for sectioning usually involves embedding in an epoxy resin. Araldite 6005 Resin and Hardener are mixed so that the hardness of the embedding medium matches that of the sample to reduce any distortion of the sample during the sectioning process. No dehydration series are needed to prepare our usual samples for embedding, but some types require hardening and staining steps. The embedded samples are sectioned with either a prototype of a Porter-Blum Microtome or an LKB Ultrotome III. Both instruments are equipped with diamond knives.In the study of photographic film, the distribution of the developed silver particles through the layer is important to the image tone and/or scattering power. Also, the morphology of the developed silver is an important factor, and cross sections will show this structure.


Author(s):  
Patrick Echlin

A number of papers have appeared recently which purport to have carried out x-ray microanalysis on fully frozen hydrated samples. It is important to establish reliable criteria to be certain that a sample is in a fully hydrated state. The morphological appearance of the sample is an obvious parameter because fully hydrated samples lack the detailed structure seen in their freeze dried counterparts. The electron scattering by ice within a frozen-hydrated section and from the surface of a frozen-hydrated fracture face obscures cellular detail. (Fig. 1G and 1H.) However, the morphological appearance alone can be quite deceptive for as Figures 1E and 1F show, parts of frozen-dried samples may also have the poor morphology normally associated with fully hydrated samples. It is only when one examines the x-ray spectra that an assurance can be given that the sample is fully hydrated.


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