1
|
Kumari L, Yadav R, Kaur D, Dey P, Bhatia A. An image analysis approach to characterize micronuclei differences in different subtypes of breast cancer. Pathol Res Pract 2024; 254:155126. [PMID: 38228038 DOI: 10.1016/j.prp.2024.155126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 01/18/2024]
Abstract
BACKGROUND Micronuclei (MN) have been used as screening, diagnostic and prognostic markers in multiple cancer types, including breast cancer (BC). However, the question that the MN present in all subtypes of BC are similar or different remains unanswered. We thus hypothesized that MN present in different subtypes of BC may differ in their contents which may be visible as differences in their morphologic and morphometric features. This study was thus carried out with the aim to identify the differences between MN morphometry, complexity, and texture in different subtypes of BC, such as estrogen and progesterone receptor-positive (ER+/PR+; MCF-7, T-47D), human epidermal growth factor receptor-positive (Her2 +;SKBR3) and triple-negative BC (TNBC; MDA-MB-231, MDA-MB-468) cell lines (CLs) by ImageJ software. METHODS For analysis of MN dimensions, MN irregularity, and texture, we used morphometry and two mathematical computer-assisted algorithms, i.e., fractal dimension (FD) and grey level co-occurrence matrix (GLCM) of ImageJ software. RESULTS MN area and perimeter values showed differences in the size of MN in different subtypes of BC, with the largest MN in TNBC CLs. GLCM parameters (entropy, angular second moment, inverse difference moment, contrast, and correlation) showed highly heterogenous texture in case of TNBC MN as compared to the others. FD analysis also revealed more complexity and irregularity in MN found in TNBC cells. CONCLUSION The study for the first time showed morphometric, architectural and texture related differences amongst MN present in different subtypes of BC. The above may reflect differences in their composition and contents. Further, these differences may point towards the distinct mechanisms involved in the formation of MN in different subtypes of BC that need to be explored further.
Collapse
Affiliation(s)
- Laxmi Kumari
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Reena Yadav
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Deepinder Kaur
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pranab Dey
- Department of Cytology and Gynaecological Pathology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Alka Bhatia
- Department of Experimental Medicine and Biotechnology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| |
Collapse
|
2
|
Miśkiewicz J, Burdach Z, Trela Z, Siemieniuk A, Karcz W. Multifractal Analysis of the Influence of Indole-3-Acetic Acid on Fast-Activating Vacuolar (FV) Channels of Beta vulgaris L. Taproot Cells. MEMBRANES 2023; 13:406. [PMID: 37103833 PMCID: PMC10141395 DOI: 10.3390/membranes13040406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
In this paper, the multifractal properties of the ion current time series in the fast-activating vacuolar (FV) channels of Beta vulgaris L. taproot cells were investigated. These channels are permeable for only monovalent cations and mediate K+ at very low concentrations of cytosolic Ca2+ and large voltages of either polarity. Using the patch clamp technique, the currents of the FV channels in red beet taproot vacuoles were recorded and analysed by using the multifractal detrended fluctuation analysis (MFDFA) method. The activity of the FV channels depended on the external potential and was sensitive to the auxin. It was also shown that the singularity spectrum of the ion current in the FV channels is non-singular, and the multifractal parameters, i.e., the generalised Hurst exponent and the singularity spectrum, were modified in the presence of IAA. Taking into account the obtained results, it can be suggested that the multifractal properties of fast-activating vacuolar (FV) K+ channels, indicating the existence of long-term memory, should be taken into account in the molecular mechanism of the auxin-induced growth of plant cells.
Collapse
Affiliation(s)
- Janusz Miśkiewicz
- Institute of Theoretical Physics, University of Wrocław, 50-204 Wrocław, Poland
- Physics and Biophysics Department, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Zbigniew Burdach
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Zenon Trela
- Physics and Biophysics Department, Wrocław University of Environmental and Life Sciences, 50-375 Wrocław, Poland
| | - Agnieszka Siemieniuk
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| | - Waldemar Karcz
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
| |
Collapse
|
3
|
Spatial constrains and information content of sub-genomic regions of the human genome. iScience 2021; 24:102048. [PMID: 33554061 PMCID: PMC7843455 DOI: 10.1016/j.isci.2021.102048] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/30/2020] [Accepted: 01/06/2021] [Indexed: 02/08/2023] Open
Abstract
Complexity metrics and machine learning (ML) models have been utilized to analyze the lengths of segmental genomic entities of DNA sequences (exonic, intronic, intergenic, repeat, unique) with the purpose to ask questions regarding the segmental organization of the human genome within the size distribution of these sequences. For this we developed an integrated methodology that is based upon the reconstructed phase space theorem, the non-extensive statistical theory of Tsallis, ML techniques, and a technical index, integrating the generated information, which we introduce and named complexity factor (COFA). Our analysis revealed that the size distribution of the genomic regions within chromosomes are not random but follow patterns with characteristic features that have been seen through its complexity character, and it is part of the dynamics of the whole genome. Finally, this picture of dynamics in DNA is recognized using ML tools for clustering, classification, and prediction with high accuracy. The lengths of DNA subgenomic entities satisfied the Tsallis non-extensive statistics The size distribution of the subgenomic entities within chromosomes follow specific patterns A technical index COFA was introduced to characterize the degree of complexity The degree of complexity behavior in DNA is identifiable using ML approaches
Collapse
|
4
|
Ahamed MRA, Babini MH, Namazi H. Complexity-based decoding of the relation between human voice and brain activity. Technol Health Care 2020; 28:665-674. [DOI: 10.3233/thc-192105] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: The human voice is the main feature of human communication. It is known that the brain controls the human voice. Therefore, there should be a relation between the characteristics of voice and brain activity. OBJECTIVE: In this research, electroencephalography (EEG) as the feature of brain activity and voice signals were simultaneously analyzed. METHOD: For this purpose, we changed the activity of the human brain by applying different odours and simultaneously recorded their voices and EEG signals while they read a text. For the analysis, we used the fractal theory that deals with the complexity of objects. The fractal dimension of EEG signal versus voice signal in different levels of brain activity were computed and analyzed. RESULTS: The results indicate that the activity of human voice is related to brain activity, where the variations of the complexity of EEG signal are linked to the variations of the complexity of voice signal. In addition, the EEG and voice signal complexities are related to the molecular complexity of applied odours. CONCLUSION: The employed method of analysis in this research can be widely applied to other physiological signals in order to relate the activities of different organs of human such as the heart to the activity of his brain.
Collapse
|
5
|
Hewelt B, Li H, Jolly MK, Kulkarni P, Mambetsariev I, Salgia R. The DNA walk and its demonstration of deterministic chaos-relevance to genomic alterations in lung cancer. Bioinformatics 2019; 35:2738-2748. [PMID: 30615123 PMCID: PMC6691335 DOI: 10.1093/bioinformatics/bty1021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 12/05/2018] [Accepted: 01/04/2019] [Indexed: 12/25/2022] Open
Abstract
MOTIVATION Advancements in cancer genetics have facilitated the development of therapies with actionable mutations. Although mutated genes have been studied extensively, their chaotic behavior has not been appreciated. Thus, in contrast to naïve DNA, mutated DNA sequences can display characteristics of unpredictability and sensitivity to the initial conditions that may be dictated by the environment, expression patterns and presence of other genomic alterations. Employing a DNA walk as a form of 2D analysis of the nucleotide sequence, we demonstrate that chaotic behavior in the sequence of a mutated gene can be predicted. RESULTS Using fractal analysis for these DNA walks, we have determined the complexity and nucleotide variance of commonly observed mutated genes in non-small cell lung cancer, and their wild-type counterparts. DNA walks for wild-type genes demonstrate varying levels of chaos, with BRAF, NTRK1 and MET exhibiting greater levels of chaos than KRAS, paxillin and EGFR. Analyzing changes in chaotic properties, such as changes in periodicity and linearity, reveal that while deletion mutations indicate a notable disruption in fractal 'self-similarity', fusion mutations demonstrate bifurcations between the two genes. Our results suggest that the fractals generated by DNA walks can yield important insights into potential consequences of these mutated genes. AVAILABILITY AND IMPLEMENTATION Introduction to Turtle graphics in Python is an open source article on learning to develop a script for Turtle graphics in Python, freely available on the web at https://docs.python.org/2/library/turtle.html. cDNA sequences were obtained through NCBI RefSeq database, an open source database that contains information on a large array of genes, such as their nucleotide and amino acid sequences, freely available at https://www.ncbi.nlm.nih.gov/refseq/. FracLac plugin for Fractal analysis in ImageJ is an open source plugin for the ImageJ program to perform fractal analysis, free to download at https://imagej.nih.gov/ij/plugins/fraclac/FLHelp/Introduction.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Blake Hewelt
- Department of Medical Oncology and Therapeutics Research
| | - Haiqing Li
- Department of Computational & Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Mohit Kumar Jolly
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore, India
| | | | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research
| |
Collapse
|
6
|
Metze K, Adam R, Florindo JB. The fractal dimension of chromatin - a potential molecular marker for carcinogenesis, tumor progression and prognosis. Expert Rev Mol Diagn 2019; 19:299-312. [DOI: 10.1080/14737159.2019.1597707] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Konradin Metze
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Randall Adam
- Department of Pathology, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - João Batista Florindo
- Department of Applied Mathematics, Institute of Mathematics, Statistics and Scientific Computing, State University of Campinas, Campinas, Brazil
| |
Collapse
|
7
|
Corona-Ruiz M, Hernandez-Cabrera F, Cantú-González JR, González-Amezcua O, Javier Almaguer F. A Stochastic Phylogenetic Algorithm for Mitochondrial DNA Analysis. Front Genet 2019; 10:66. [PMID: 30906309 PMCID: PMC6418022 DOI: 10.3389/fgene.2019.00066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 01/28/2019] [Indexed: 11/13/2022] Open
Abstract
This paper presents an exploratory analysis of the mitochondrial DNA (mtDNA) of 32 species in the subphylum Vertebrata, divided in 7 taxonomic classes. Multiple stochastic parameters, such as the Hurst and detrended fluctuation analysis (DFA) exponents, Shannon entropy, and Chargaff ratio are computed for each DNA sequence. The biological interpretation of these parameters leads to defining a triplet of novel indices. These new functions incorporate the long-range correlations, the probability of occurrence of nucleic bases, and the ratio of pyrimidines-to-purines. Results suggest that relevant regions in mtDNA can be located using the proposed indices. Furthermore, early results from clustering algorithms indicate that the indices introduced might be useful in phylogenetic studies.
Collapse
Affiliation(s)
- M Corona-Ruiz
- Facultad de Ciencias Físico-Matemáticas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Francisco Hernandez-Cabrera
- Facultad de Ciencias Físico-Matemáticas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | | | - O González-Amezcua
- Facultad de Ciencias Físico-Matemáticas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Francisco Javier Almaguer
- Facultad de Ciencias Físico-Matemáticas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| |
Collapse
|
8
|
Complexity-Based Analysis of the Difference Between Normal Subjects and Subjects with Stuttering in Speech Evoked Auditory Brainstem Response. J Med Biol Eng 2018. [DOI: 10.1007/s40846-018-0430-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
9
|
Azar FE, Azami-Aghdash S, Pournaghi-Azar F, Mazdaki A, Rezapour A, Ebrahimi P, Yousefzadeh N. Cost-effectiveness of lung cancer screening and treatment methods: a systematic review of systematic reviews. BMC Health Serv Res 2017; 17:413. [PMID: 28629461 PMCID: PMC5477275 DOI: 10.1186/s12913-017-2374-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 06/09/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Due to extensive literature in the field of lung cancer and their heterogeneous results, the aim of this study was to systematically review of systematic reviews studies which reviewed the cost-effectiveness of various lung cancer screening and treatment methods. METHODS In this systematic review of systematic reviews study, required data were collected searching the following key words which selected from Mesh: "lung cancer", "lung oncology", "lung Carcinoma", "lung neoplasm", "lung tumors", "cost- effectiveness", "systematic review" and "Meta-analysis". The following databases were searched: PubMed, Cochrane Library electronic databases, Google Scholar, and Scopus. Two reviewers (RA and A-AS) evaluated the articles according to the checklist of "assessment of multiple systematic reviews" (AMSTAR) tool. RESULTS Overall, information of 110 papers was discussed in eight systematic reviews. Authors focused on cost-effectiveness of lung cancer treatments in five systematic reviews. Targeted therapy options (bevacizumab, Erlotinib and Crizotinib) show an acceptable cost-effectiveness. Results of three studies failed to show cost-effectiveness of screening methods. None of the studies had used the meta-analysis method. The Quality of Health Economic Studies (QHES) tool and Drummond checklist were mostly used in assessing the quality of articles. Most perspective was related to the Payer (64 times) and the lowest was related to Social (11times). Most cases referred to Incremental analysis (82%) and also the lowest point of referral was related to Discounting (in 49% of the cases). The average quality score of included studies was calculated 9.2% from 11. CONCLUSIONS Targeted therapy can be an option for the treatment of lung cancer. Evaluation of the cost-effectiveness of computerized tomographic colonography (CTC) in lung cancer screening is recommended. The perspective of the community should be more taken into consideration in studies of cost-effectiveness. Paying more attention to the topic of Discounting will be necessary in the studies.
Collapse
Affiliation(s)
| | - Saber Azami-Aghdash
- Road Traffic Injury Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Pournaghi-Azar
- Dental and Periodental Research Centre, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Mazdaki
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Aziz Rezapour
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran.
| | - Parvin Ebrahimi
- Department of Health service Management, School of Health Management and Information Sciences & Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Negar Yousefzadeh
- Health Management and Economics Research Center, Iran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
10
|
Namazi H, Akrami A, Hussaini J, Silva ON, Wong A, Kulish VV. The fractal based analysis of human face and DNA variations during aging. Biosci Trends 2016; 10:477-481. [PMID: 27795483 DOI: 10.5582/bst.2016.01182] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Human DNA is the main unit that shapes human characteristics and features such as behavior. Thus, it is expected that changes in DNA (DNA mutation) influence human characteristics and features. Face is one of the human features which is unique and also dependent on his gen. In this paper, for the first time we analyze the variations of human DNA and face simultaneously. We do this job by analyzing the fractal dimension of DNA walk and face during human aging. The results of this study show the human DNA and face get more complex by aging. These complexities are mapped on fractal exponents of DNA walk and human face. The method discussed in this paper can be further developed in order to investigate the direct influence of DNA mutation on the face variations during aging, and accordingly making a model between human face fractality and the complexity of DNA walk.
Collapse
Affiliation(s)
- Hamidreza Namazi
- School of Mechanical and Aerospace Engineering, Nanyang Technological University
| | | | | | | | | | | |
Collapse
|
11
|
Namazi H, Khosrowabadi R, Hussaini J, Habibi S, Farid AA, Kulish VV. Analysis of the influence of memory content of auditory stimuli on the memory content of EEG signal. Oncotarget 2016; 7:56120-56128. [PMID: 27528219 PMCID: PMC5302900 DOI: 10.18632/oncotarget.11234] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/29/2016] [Indexed: 11/25/2022] Open
Abstract
One of the major challenges in brain research is to relate the structural features of the auditory stimulus to structural features of Electroencephalogram (EEG) signal. Memory content is an important feature of EEG signal and accordingly the brain. On the other hand, the memory content can also be considered in case of stimulus. Beside all works done on analysis of the effect of stimuli on human EEG and brain memory, no work discussed about the stimulus memory and also the relationship that may exist between the memory content of stimulus and the memory content of EEG signal. For this purpose we consider the Hurst exponent as the measure of memory. This study reveals the plasticity of human EEG signals in relation to the auditory stimuli. For the first time we demonstrated that the memory content of an EEG signal shifts towards the memory content of the auditory stimulus used. The results of this analysis showed that an auditory stimulus with higher memory content causes a larger increment in the memory content of an EEG signal. For the verification of this result, we benefit from approximate entropy as indicator of time series randomness. The capability, observed in this research, can be further investigated in relation to human memory.
Collapse
Affiliation(s)
- Hamidreza Namazi
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore
| | - Reza Khosrowabadi
- Institute for Cognitive and Brain Science, Shahid Beheshti University, Tehran, Iran
| | - Jamal Hussaini
- Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh, Selangor, Malaysia
| | | | - Ali Akhavan Farid
- Faculty of Engineering and Technology, Multimedia University, Melaka, Malaysia
| | - Vladimir V. Kulish
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore
| |
Collapse
|
12
|
Mathematical Modelling and Prediction of the Effect of Chemotherapy on Cancer Cells. Sci Rep 2015; 5:13583. [PMID: 26316014 PMCID: PMC4552002 DOI: 10.1038/srep13583] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/03/2015] [Indexed: 01/17/2023] Open
Abstract
Cancer is a class of diseases characterized by out-of-control cells' growth which affect DNAs and make them damaged. Many treatment options for cancer exist, with the primary ones including surgery, chemotherapy, radiation therapy, hormonal therapy, targeted therapy and palliative care. Which treatments are used depends on the type, location, and grade of the cancer as well as the person's health and wishes. Chemotherapy is the use of medication (chemicals) to treat disease. More specifically, chemotherapy typically refers to the destruction of cancer cells. Considering the diffusion of drugs in cancer cells and fractality of DNA walks, in this research we worked on modelling and prediction of the effect of chemotherapy on cancer cells using Fractional Diffusion Equation (FDE). The employed methodology is useful not only for analysis of the effect of special drug and cancer considered in this research but can be expanded in case of different drugs and cancers.
Collapse
|