Abstract:
:Anthrax is one of the important diseases in humans and animals, caused by the gram-positive bacteria spores called Bacillus anthracis. The disease is still one of the health problems of developing countries. Due to fatigue and decreased visual acuity, microscopic diagnosis of diseases by humans may not be of good quality. In this paper, for the first time, a system for automatic and rapid diagnosis of anthrax disease simultaneously with detection and segmentation of B. anthracis bacteria in microscopic images has been proposed based on artificial intelligence and deep learning techniques. Two important architectures of deep neural networks including UNet and UNet++ have been used for detection and segmentation of the most important component of the image i.e. bacteria. Automated detection and segmentation of B. anthracis bacteria offers the same level of accuracy as the human diagnostic specialist and in some cases outperforms it. Experimental results show that these deep architectures especially UNet++ can be used effectively and efficiently to automate B. anthracis bacteria segmentation of microscopic images obtained under different conditions. UNet++ produces outstanding results despite the many challenges in this field, such as high image dimension, image artifacts, object crowding, and overlapping. We conducted our experiments on a dataset prepared privately and achieved an accuracy of 97% and the dice score of 0.96 on the patch test images. It also tested on whole raw images and a recall of 98% and accuracy of 97% is achieved, which shows excellent performance in the bacteria segmentation task. The low cost and high speed of diagnosis and no need for a specialist are other benefits of the proposed system.
journal_name
J Microbiol Methodsjournal_title
Journal of microbiological methodsauthors
Hoorali F,Khosravi H,Moradi Bdoi
10.1016/j.mimet.2020.106056subject
Has Abstractpub_date
2020-10-01 00:00:00pages
106056eissn
0167-7012issn
1872-8359pii
S0167-7012(20)30772-7journal_volume
177pub_type
杂志文章abstract::Viability PCR (v-PCR) as a method to selectively detect intact live cells has gained considerable interest over the last years with an increasing number of applications. The principle is based on treatment of microbiological samples with a viability dye prior to extraction of genomic DNA and its amplification. The dye...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2013.01.018
更新日期:2013-04-01 00:00:00
abstract::Plant-associated bacteria produce quorum sensing (QS) signals for community (biofilm) formation and functioning in the rhizosphere. The QS-positive biofilm-forming rhizobacteria that excel benefits to the plants are now gaining increased importance for agricultural use due to their high competitiveness. However, there...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2018.11.018
更新日期:2019-01-01 00:00:00
abstract::Linear B-cell epitopes ((93)AKEFEAAAL(101) and (66)PQLTDVLN(73)) of CfaB were genetically fused to ltb-(gly)5-cfaB(1-25). Sera of rabbits immunized with fusion proteins reacted strongly with solid-phase bound ETEC bacteria bearing CFA/I fimbriae. Sera failed to agglutinate or inhibit hemagglutination promoted by CFA/I...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.07.035
更新日期:2014-11-01 00:00:00
abstract::In this study the influence of X-ray computed tomography (XRCT) on the microbial community structure and function in soils has been investigated. Our results clearly indicate that XRCT of soil samples has a strong impact on microbial communities and changes structure and function significantly due to the death of sele...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2013.02.009
更新日期:2013-05-01 00:00:00
abstract::Leptospirosis is an emerging worldwide zoonosis with a changing epidemiology responsible for an acute disease in humans and dogs. A better knowledge of the responsible bacterium Leptospira and in particular its various serovars and serogroups prevalence is essential for better diagnosis and prevention of the disease. ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2020.106007
更新日期:2020-09-01 00:00:00
abstract::A new cloning vector, pTcp216M-MCS, containing an engineered esterase ESTL120P as an indicator was constructed for the screening of positive clones harboring recombinant plasmids. After cloning the mutant esterase gene into pTrc99A, a synthetic multiple cloning site (MCS) was inserted into the predicted gaps of the es...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2009.03.010
更新日期:2009-06-01 00:00:00
abstract::Although methods such as spectrophotometry are useful for identifying growth differences among bacterial strains, it is currently difficult to similarly determine whether bacteriophage strains differ in growth using high throughput methods. Here we use automated spectrophotometry to develop an in vitro method for indi...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2011.10.020
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:In a two-stage exchange protocol for prosthetic joint infection (PJI), bacteria surviving over the antibiotic-loaded cement spacers may cause the persistence of infection with renewed clinical symptoms following the surgery. Culture after sonication of removed prosthesis is more sensitive than conventional p...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2018.12.006
更新日期:2019-01-01 00:00:00
abstract::This study investigated the various commercially available kits and 'in-house' methods to extract DNA from Gram-negative and Gram-positive bacteria, yeast and fungal agents in commonly employed blood culture material. The main methods investigated were as follows; Qiagen QIAmp Blood kit, Roche high PCR template prepar...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(00)00174-3
更新日期:2000-10-01 00:00:00
abstract::Bacterial fruit blotch (BFB) of cucurbits, caused by Acidovorax citrulli, is a major threat to commercial watermelon and melon production worldwide. At present, there are at least two genetically distinct sub-populations (group I and II) of A. citrulli that differ in host preference among cucurbit species and copper s...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2019.02.003
更新日期:2019-03-01 00:00:00
abstract::Cryptosporidium parvum is an enteric coccidian parasite that is recognised as a frequent cause of water-borne disease in humans. We report for the first time on use of the in vitro HCT-8 cell culture-quantitative PCR (qPCR) assay and the in vivo SCID-mouse bioassay for evaluating critical factors that reduce or elimin...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2010.01.017
更新日期:2010-03-01 00:00:00
abstract::A simple and sensitive method based on the use of colloidal chitin stained with Remazol Brilliant Blue R (RBB) is proposed to evaluate chitinase activity. If this colloidal-stained substrate is included as a carbon source in a liquid medium, this technique allows the selection or the comparison of chitinolytic microor...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2003.10.011
更新日期:2004-02-01 00:00:00
abstract::The basic requirement of human beings is better health but the serious health effects and numerous infections caused by rapid growth of harmful pathogens resulting in a large number of deaths and is a significant challenge to modern science. Microbes infecting humans can be stopped in two ways: disinfectants and antim...
journal_title:Journal of microbiological methods
pub_type: 杂志文章,评审
doi:10.1016/j.mimet.2019.105650
更新日期:2019-08-01 00:00:00
abstract::Permanent staining of faecal smears by Wheatley's trichrome technique has been used by many scientists for the detection of parasites in the past and it was found to be highly sensitive. This study was conducted to evaluate the use of Wintergreen oil in comparison with xylene in Wheatley's trichrome staining technique...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2012.08.004
更新日期:2012-10-01 00:00:00
abstract::Expressed sequence tags (ESTs) from fungal-infected plant tissues are composed of a mixture of plant and fungal sequences. Using freely available software and tools, a novel procedure is described for distinguishing plant and fungal DNA sequences. Although the GenBank non-redundant (NR) database is larger and therefor...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(03)00067-8
更新日期:2003-09-01 00:00:00
abstract::Thanks to their photosynthetic and nutritive properties, cyanobacteria of the Arthrospira genus are of interest as food supplements, as efficient oxygen producing life support system organisms for manned space flight, and for the production of biofuels. Despite these potential valuable applications, full genome sequen...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2009.11.012
更新日期:2010-02-01 00:00:00
abstract::Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal RNA gene amplicons was used to study the stool microbiota of hospitalized patients and to examine the effect of antibiotic therapy. For one patient, 16 anaerobic species identified by random cloning and sequencing of PCR-amplified rRNA genes fro...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(03)00059-9
更新日期:2003-08-01 00:00:00
abstract::Limited biological samples of microbial origin often yield insufficient amounts of genomic DNA, making application of standard techniques of genetic analysis, like amplified fragment length polymorphism (AFLP), virtually impossible. The Phi29 DNA polymerase based whole genome amplification (WGA) method has the potenti...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.03.009
更新日期:2005-11-01 00:00:00
abstract::Effective biolistic transformation of intact conidia from the filamentous fungus Trichoderma reesei was achieved using the Bio-Rad Hepta Adaptor system with seven barrels for particle launch. Transformation frequencies of up to 39 colonies per microg of circular DNA and 37 colonies per microg of linear DNA were obtain...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(02)00126-4
更新日期:2002-11-01 00:00:00
abstract::Fluorescence in situ hybridization (FISH) can provide information on the morphology, spatial arrangement, and local environment of individual cells enabling the investigation of intact microbial communities. GeneFISH uses polynucleotide probes and enzymatic signal amplification to detect genes that are present in low ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2021.106147
更新日期:2021-01-22 00:00:00
abstract::Using robotics and the MPN technique, a 96-microwell method was developed to compare two procedures for enumeration of viable chlorine-treated B. atrophaeus spores: broth-culture enrichment followed by real-time polymerase chain reaction analysis; and filter plating on agar. Recoveries of chlorine-treated spores were ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.07.011
更新日期:2007-10-01 00:00:00
abstract::As part of a major European research project, a diagnostic PCR assay, including an internal amplification control, was developed and validated in a collaborative trial for the detection of Escherichia coli O157. The assay is based on amplification of sequences of the rfbE O157 gene. The collaborative trial, including ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章,多中心研究
doi:10.1016/j.mimet.2003.08.012
更新日期:2003-12-01 00:00:00
abstract::The spore is the form released in a bioterrorism attack. There is a real need for definition of new targets for Bacillus anthracis that might be incorporated into emerging biodetection technologies. Particularly of interest are macromolecules found in B. anthracis that are (1) spore-specific, (2) readily accessible on...
journal_title:Journal of microbiological methods
pub_type: 杂志文章,评审
doi:10.1016/s0167-7012(03)00095-2
更新日期:2003-08-01 00:00:00
abstract::We have developed a software tool, GenomeComp, for summarizing, parsing and visualizing the genome sequences comparison results derived from voluminous BLAST textual output. With GenomeComp, the variation between genomes can be easily highlighted, such as repeat regions, insertions, deletions and rearrangements of gen...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/s0167-7012(03)00094-0
更新日期:2003-09-01 00:00:00
abstract::Quantification of invasive, intracellular bacteria is critical in many areas of cellular microbiology and immunology. We describe a novel and fast approach to determine invasion of bacterial pathogens in adherent cell types such as epithelial cells or fibroblasts based on flow cytometry. Using the CEACAM-mediated upta...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.08.013
更新日期:2006-05-01 00:00:00
abstract::Actinomyces naeslundii is an early colonizer with important roles in the development of the oral biofilm. The effects of butyric acid, one of short chain fatty acids in A. naeslundii biofilm formation was observed using a flow cell system with Tryptic soy broth without dextrose and with 0.25% sucrose (TSB sucrose). Si...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2014.12.021
更新日期:2015-02-01 00:00:00
abstract::Streptococcus agalactiae, group B streptococci (GBS) is the leading cause of severe bacterial infections in newborns. GBS expression studies allowed the identification and characterization of virulence factors and a better understanding of the host-pathogen-environment interactions. The measurement of transcript level...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2012.05.011
更新日期:2012-09-01 00:00:00
abstract::Aggregatibacter (A.) actinomycetemcomitans is a periodontopathogenic bacterium causing aggressive periodontitis. Here we describe a single-step transconjugation system as novel and easily applicable protocol for site-specific genetic manipulation of A. actinomycetemcomitans. Deletion of PgaC, which is involved in the ...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2018.04.002
更新日期:2018-05-01 00:00:00
abstract::Technique for immobilization using sodium alginate as the matrix to preserve Bacillus thuringiensis var. israelensis isolates for long time storage was developed. Two strains of B. thuringiensis var. israelensis viz., VCRC B-17 and WHO standard strain IPS-82 were immobilized in alginate matrix and preserved at 4 degre...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2007.11.001
更新日期:2008-01-01 00:00:00
abstract::An effective microbial preservation technology for the long-term storage of viable prokaryotic cells is described. The method combines an almost instantaneous drying step with minimal stress to the cells during drying to maximize survival on rehydration. This is achieved by contact of a microlitre aliquot of a bacteri...
journal_title:Journal of microbiological methods
pub_type: 杂志文章
doi:10.1016/j.mimet.2005.02.014
更新日期:2005-10-01 00:00:00